[Bioperl-l] Problems with BioPerl-1.4
Wolf-Gerolf Thies
thies at itg.fzk.de
Mon Mar 1 11:40:29 EST 2004
Dear BioPerl experts,
I have tried to install BioPerl-1.4 on on True64UNIX (OSF-1) Version 5.1.
The standard make fails with the error:
Make: line too long. Stop.
Then I have tested the gnu make, but it also fails:
# /usr/local/bin/make
mkdir blib
mkdir blib/lib
mkdir blib/arch
mkdir blib/arch/auto
mkdir blib/arch/auto/Bio
mkdir blib/lib/auto
mkdir blib/lib/auto/Bio
mkdir blib/man1
mkdir blib/man3
make: execvp: /bin/sh: Arg list too long
make: *** [pm_to_blib] Error 127
Do you have any idea what might be my problem ? I join the makefile
to this mail.
With kind regards
Wolf-Gerolf Thies
-------------- next part --------------
# This Makefile is for the Bio extension to perl.
#
# It was generated automatically by MakeMaker version
# 5.45 (Revision: 1.222) from the contents of
# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
#
# ANY CHANGES MADE HERE WILL BE LOST!
#
# MakeMaker ARGV: ()
#
# MakeMaker Parameters:
# ABSTRACT => q[Bioinformatics Toolkit]
# AUTHOR => q[Bioperl Team (bioperl-l at bioperl.org)]
# DIR => []
# DISTNAME => q[bioperl]
# EXE_FILES => [q[./scripts_temp/bp_load_gff.pl], q[./scripts_temp/bp_genbank2gff.pl], q[./scripts_temp/bp_bulk_load_gff.pl], q[./scripts_temp/bp_fast_load_gff.pl], q[./scripts_temp/bp_generate_histogram.pl], q[./scripts_temp/bp_pg_bulk_load_gff.pl], q[./scripts_temp/bp_process_gadfly.pl], q[./scripts_temp/bp_process_ncbi_human.pl], q[./scripts_temp/bp_process_sgd.pl], q[./scripts_temp/bp_process_wormbase.pl], q[./scripts_temp/bp_biofetch_genbank_proxy.pl], q[./scripts_temp/bp_bioflat_index.pl], q[./scripts_temp/bp_biogetseq.pl], q[./scripts_temp/bp_flanks.pl], q[./scripts_temp/bp_biblio.pl], q[./scripts_temp/bp_frend.pl], q[./scripts_temp/bp_feature_draw.pl], q[./scripts_temp/bp_search_overview.pl], q[./scripts_temp/bp_fetch.pl], q[./scripts_temp/bp_index.pl], q[./scripts_temp/bp_composite_LD.pl], q[./scripts_temp/bp_heterogeneity_test.pl], q[./scripts_temp/bp_filter_search.pl], q[./scripts_temp/bp_extract_feature_seq.pl], q[./scripts_temp/bp_seqconvert.pl], q[./scripts_temp/bp_split_seq.pl], q[./scripts_temp/bp_translate_seq.pl], q[./scripts_temp/bp_aacomp.pl], q[./scripts_temp/bp_chaos_plot.pl], q[./scripts_temp/bp_gccalc.pl], q[./scripts_temp/bp_oligo_count.pl], q[./scripts_temp/bp_local_taxonomydb_query.pl], q[./scripts_temp/bp_taxid4species.pl], q[./scripts_temp/bp_blast2tree.pl], q[./scripts_temp/bp_nrdb.pl], q[./scripts_temp/bp_mrtrans.pl], q[./scripts_temp/bp_sreformat.pl], q[./scripts_temp/bp_dbsplit.pl], q[./scripts_temp/bp_mask_by_search.pl], q[./scripts_temp/bp_mutate.pl], q[./scripts_temp/bp_pairwise_kaks.pl], q[./scripts_temp/bp_remote_blast.pl], q[./scripts_temp/bp_search2BSML.pl], q[./scripts_temp/bp_search2alnblocks.pl], q[./scripts_temp/bp_search2gff.pl], q[./scripts_temp/bp_search2tribe.pl], q[./scripts_temp/bp_seq_length.pl]]
# NAME => q[Bio]
# PL_FILES => { doc/makedoc.PL=>[q[bioscripts.pod], q[biodatabases.pod], q[biodesign.pod], q[bioperl.pod]] }
# PREREQ_PM => { HTML::Entities=>q[0], File::Spec=>q[0], File::Temp=>q[0], DB_File=>q[0], IO::Scalar=>q[0], IO::String=>q[0] }
# VERSION_FROM => q[Bio/Root/Version.pm]
# dist => { DIST_DEFAULT=>q[all tardist], COMPRESS=>q[gzip -9f], SUFFIX=>q[.gz] }
# realclean => { FILES=>q[./Seq.pm.bak] }
# --- MakeMaker post_initialize section:
# --- MakeMaker const_config section:
# These definitions are from config.sh (via /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/Config.pm)
# They may have been overridden via Makefile.PL or on the command line
AR = ar
CC = cc
CCCDLFLAGS =
CCDLFLAGS = -Wl,-rpath,/usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE
DLEXT = so
DLSRC = dl_dlopen.xs
LD = ld
LDDLFLAGS = -shared -expect_unresolved "*" -O4 -msym -std -s
LDFLAGS =
LIBC = /usr/shlib/libc.so
LIB_EXT = .a
OBJ_EXT = .o
OSNAME = dec_osf
OSVERS = 5.1
RANLIB = :
SO = so
EXE_EXT =
FULL_AR = /usr/bin/ar
# --- MakeMaker constants section:
AR_STATIC_ARGS = cr
NAME = Bio
DISTNAME = bioperl
NAME_SYM = Bio
VERSION = 1.4
VERSION_SYM = 1_4
XS_VERSION = 1.4
INST_BIN = blib/bin
INST_EXE = blib/script
INST_LIB = blib/lib
INST_ARCHLIB = blib/arch
INST_SCRIPT = blib/script
PREFIX = /usr/lib/perl-5.6.0
INSTALLDIRS = site
INSTALLPRIVLIB = $(PREFIX)/lib/5.6.0
INSTALLARCHLIB = $(PREFIX)/lib/5.6.0/alpha-dec_osf
INSTALLSITELIB = $(PREFIX)/lib/site_perl/5.6.0
INSTALLSITEARCH = $(PREFIX)/lib/site_perl/5.6.0/alpha-dec_osf
INSTALLBIN = $(PREFIX)/bin
INSTALLSCRIPT = $(PREFIX)/bin
PERL_LIB = /usr/lib/perl-5.6.0/lib/5.6.0
PERL_ARCHLIB = /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf
SITELIBEXP = /usr/lib/perl-5.6.0/lib/site_perl/5.6.0
SITEARCHEXP = /usr/lib/perl-5.6.0/lib/site_perl/5.6.0/alpha-dec_osf
LIBPERL_A = libperl.a
FIRST_MAKEFILE = Makefile
MAKE_APERL_FILE = Makefile.aperl
PERLMAINCC = $(CC)
PERL_INC = /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE
PERL = /usr/bin/perl
FULLPERL = /usr/bin/perl
FULL_AR = /usr/bin/ar
VERSION_MACRO = VERSION
DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
XS_VERSION_MACRO = XS_VERSION
XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
MAKEMAKER = /usr/lib/perl-5.6.0/lib/5.6.0/ExtUtils/MakeMaker.pm
MM_VERSION = 5.45
# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
# ROOTEXT = Directory part of FULLEXT with leading slash (eg /DBD) !!! Deprecated from MM 5.32 !!!
# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
FULLEXT = Bio
BASEEXT = Bio
DLBASE = $(BASEEXT)
VERSION_FROM = Bio/Root/Version.pm
OBJECT =
LDFROM = $(OBJECT)
LINKTYPE = dynamic
# Handy lists of source code files:
XS_FILES=
C_FILES =
O_FILES =
H_FILES =
HTMLLIBPODS =
HTMLSCRIPTPODS =
MAN1PODS = ./scripts_temp/bp_aacomp.pl \
./scripts_temp/bp_biblio.pl \
./scripts_temp/bp_biofetch_genbank_proxy.pl \
./scripts_temp/bp_biogetseq.pl \
./scripts_temp/bp_blast2tree.pl \
./scripts_temp/bp_bulk_load_gff.pl \
./scripts_temp/bp_chaos_plot.pl \
./scripts_temp/bp_composite_LD.pl \
./scripts_temp/bp_dbsplit.pl \
./scripts_temp/bp_extract_feature_seq.pl \
./scripts_temp/bp_fast_load_gff.pl \
./scripts_temp/bp_feature_draw.pl \
./scripts_temp/bp_fetch.pl \
./scripts_temp/bp_filter_search.pl \
./scripts_temp/bp_flanks.pl \
./scripts_temp/bp_frend.pl \
./scripts_temp/bp_gccalc.pl \
./scripts_temp/bp_genbank2gff.pl \
./scripts_temp/bp_generate_histogram.pl \
./scripts_temp/bp_heterogeneity_test.pl \
./scripts_temp/bp_index.pl \
./scripts_temp/bp_load_gff.pl \
./scripts_temp/bp_local_taxonomydb_query.pl \
./scripts_temp/bp_mask_by_search.pl \
./scripts_temp/bp_mrtrans.pl \
./scripts_temp/bp_mutate.pl \
./scripts_temp/bp_nrdb.pl \
./scripts_temp/bp_oligo_count.pl \
./scripts_temp/bp_pairwise_kaks.pl \
./scripts_temp/bp_pg_bulk_load_gff.pl \
./scripts_temp/bp_process_gadfly.pl \
./scripts_temp/bp_process_ncbi_human.pl \
./scripts_temp/bp_process_sgd.pl \
./scripts_temp/bp_process_wormbase.pl \
./scripts_temp/bp_remote_blast.pl \
./scripts_temp/bp_search2BSML.pl \
./scripts_temp/bp_search2alnblocks.pl \
./scripts_temp/bp_search2gff.pl \
./scripts_temp/bp_search2tribe.pl \
./scripts_temp/bp_search_overview.pl \
./scripts_temp/bp_seq_length.pl \
./scripts_temp/bp_seqconvert.pl \
./scripts_temp/bp_split_seq.pl \
./scripts_temp/bp_sreformat.pl \
./scripts_temp/bp_taxid4species.pl \
./scripts_temp/bp_translate_seq.pl
MAN3PODS = Bio/Align/AlignI.pm \
Bio/Align/DNAStatistics.pm \
Bio/Align/PairwiseStatistics.pm \
Bio/Align/StatisticsI.pm \
Bio/Align/Utilities.pm \
Bio/AlignIO.pm \
Bio/AlignIO/bl2seq.pm \
Bio/AlignIO/clustalw.pm \
Bio/AlignIO/emboss.pm \
Bio/AlignIO/fasta.pm \
Bio/AlignIO/maf.pm \
Bio/AlignIO/mase.pm \
Bio/AlignIO/mega.pm \
Bio/AlignIO/meme.pm \
Bio/AlignIO/metafasta.pm \
Bio/AlignIO/msf.pm \
Bio/AlignIO/nexus.pm \
Bio/AlignIO/pfam.pm \
Bio/AlignIO/phylip.pm \
Bio/AlignIO/prodom.pm \
Bio/AlignIO/psi.pm \
Bio/AlignIO/selex.pm \
Bio/AlignIO/stockholm.pm \
Bio/AnalysisI.pm \
Bio/AnalysisParserI.pm \
Bio/AnalysisResultI.pm \
Bio/AnnotatableI.pm \
Bio/Annotation/AnnotationFactory.pm \
Bio/Annotation/Collection.pm \
Bio/Annotation/Comment.pm \
Bio/Annotation/DBLink.pm \
Bio/Annotation/OntologyTerm.pm \
Bio/Annotation/Reference.pm \
Bio/Annotation/SimpleValue.pm \
Bio/Annotation/StructuredValue.pm \
Bio/Annotation/TypeManager.pm \
Bio/AnnotationCollectionI.pm \
Bio/AnnotationI.pm \
Bio/Assembly/Contig.pm \
Bio/Assembly/ContigAnalysis.pm \
Bio/Assembly/IO.pm \
Bio/Assembly/IO/ace.pm \
Bio/Assembly/IO/phrap.pm \
Bio/Assembly/Scaffold.pm \
Bio/Assembly/ScaffoldI.pm \
Bio/Biblio.pm \
Bio/Biblio/Article.pm \
Bio/Biblio/BiblioBase.pm \
Bio/Biblio/Book.pm \
Bio/Biblio/BookArticle.pm \
Bio/Biblio/IO.pm \
Bio/Biblio/IO/medline2ref.pm \
Bio/Biblio/IO/medlinexml.pm \
Bio/Biblio/IO/pubmed2ref.pm \
Bio/Biblio/IO/pubmedxml.pm \
Bio/Biblio/Journal.pm \
Bio/Biblio/JournalArticle.pm \
Bio/Biblio/MedlineArticle.pm \
Bio/Biblio/MedlineBook.pm \
Bio/Biblio/MedlineBookArticle.pm \
Bio/Biblio/MedlineJournal.pm \
Bio/Biblio/MedlineJournalArticle.pm \
Bio/Biblio/Organisation.pm \
Bio/Biblio/Patent.pm \
Bio/Biblio/Person.pm \
Bio/Biblio/Proceeding.pm \
Bio/Biblio/Provider.pm \
Bio/Biblio/PubmedArticle.pm \
Bio/Biblio/PubmedBookArticle.pm \
Bio/Biblio/PubmedJournalArticle.pm \
Bio/Biblio/Ref.pm \
Bio/Biblio/Service.pm \
Bio/Biblio/TechReport.pm \
Bio/Biblio/Thesis.pm \
Bio/Biblio/WebResource.pm \
Bio/Cluster/ClusterFactory.pm \
Bio/Cluster/FamilyI.pm \
Bio/Cluster/SequenceFamily.pm \
Bio/Cluster/UniGene.pm \
Bio/Cluster/UniGeneI.pm \
Bio/ClusterI.pm \
Bio/ClusterIO.pm \
Bio/ClusterIO/dbsnp.pm \
Bio/ClusterIO/unigene.pm \
Bio/CodonUsage/IO.pm \
Bio/CodonUsage/Table.pm \
Bio/Coordinate/Chain.pm \
Bio/Coordinate/Collection.pm \
Bio/Coordinate/ExtrapolatingPair.pm \
Bio/Coordinate/GeneMapper.pm \
Bio/Coordinate/Graph.pm \
Bio/Coordinate/MapperI.pm \
Bio/Coordinate/Pair.pm \
Bio/Coordinate/Result.pm \
Bio/Coordinate/Result/Gap.pm \
Bio/Coordinate/Result/Match.pm \
Bio/Coordinate/ResultI.pm \
Bio/Coordinate/Utils.pm \
Bio/DB/Ace.pm \
Bio/DB/Biblio/biofetch.pm \
Bio/DB/Biblio/soap.pm \
Bio/DB/BiblioI.pm \
Bio/DB/BioFetch.pm \
Bio/DB/CUTG.pm \
Bio/DB/DBFetch.pm \
Bio/DB/EMBL.pm \
Bio/DB/Failover.pm \
Bio/DB/Fasta.pm \
Bio/DB/FileCache.pm \
Bio/DB/Flat.pm \
Bio/DB/Flat/BDB.pm \
Bio/DB/Flat/BDB/embl.pm \
Bio/DB/Flat/BDB/fasta.pm \
Bio/DB/Flat/BDB/genbank.pm \
Bio/DB/Flat/BDB/swiss.pm \
Bio/DB/Flat/BDB/swissprot.pm \
Bio/DB/Flat/BinarySearch.pm \
Bio/DB/GDB.pm \
Bio/DB/GFF.pm \
Bio/DB/GFF/Adaptor/ace.pm \
Bio/DB/GFF/Adaptor/biofetch.pm \
Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
Bio/DB/GFF/Adaptor/dbi.pm \
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
Bio/DB/GFF/Adaptor/dbi/iterator.pm \
Bio/DB/GFF/Adaptor/dbi/mysql.pm \
Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
Bio/DB/GFF/Adaptor/dbi/oracle.pm \
Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
Bio/DB/GFF/Adaptor/dbi/pg.pm \
Bio/DB/GFF/Adaptor/memory.pm \
Bio/DB/GFF/Adaptor/memory_iterator.pm \
Bio/DB/GFF/Aggregator.pm \
Bio/DB/GFF/Aggregator/alignment.pm \
Bio/DB/GFF/Aggregator/clone.pm \
Bio/DB/GFF/Aggregator/coding.pm \
Bio/DB/GFF/Aggregator/match.pm \
Bio/DB/GFF/Aggregator/none.pm \
Bio/DB/GFF/Aggregator/processed_transcript.pm \
Bio/DB/GFF/Aggregator/transcript.pm \
Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
Bio/DB/GFF/Featname.pm \
Bio/DB/GFF/Feature.pm \
Bio/DB/GFF/Homol.pm \
Bio/DB/GFF/RelSegment.pm \
Bio/DB/GFF/Segment.pm \
Bio/DB/GFF/Typename.pm \
Bio/DB/GFF/Util/Binning.pm \
Bio/DB/GFF/Util/Rearrange.pm \
Bio/DB/GenBank.pm \
Bio/DB/GenPept.pm \
Bio/DB/InMemoryCache.pm \
Bio/DB/MeSH.pm \
Bio/DB/NCBIHelper.pm \
Bio/DB/Query/GenBank.pm \
Bio/DB/Query/WebQuery.pm \
Bio/DB/QueryI.pm \
Bio/DB/RandomAccessI.pm \
Bio/DB/RefSeq.pm \
Bio/DB/Registry.pm \
Bio/DB/SeqI.pm \
Bio/DB/SwissProt.pm \
Bio/DB/Taxonomy.pm \
Bio/DB/Taxonomy/entrez.pm \
Bio/DB/Taxonomy/flatfile.pm \
Bio/DB/Universal.pm \
Bio/DB/UpdateableSeqI.pm \
Bio/DB/WebDBSeqI.pm \
Bio/DB/XEMBL.pm \
Bio/DB/XEMBLService.pm \
Bio/DBLinkContainerI.pm \
Bio/Das/FeatureTypeI.pm \
Bio/Das/SegmentI.pm \
Bio/DasI.pm \
Bio/DescribableI.pm \
Bio/Event/EventGeneratorI.pm \
Bio/Event/EventHandlerI.pm \
Bio/Expression/FeatureGroup.pm \
Bio/Expression/FeatureI.pm \
Bio/Factory/AnalysisI.pm \
Bio/Factory/ApplicationFactoryI.pm \
Bio/Factory/DriverFactory.pm \
Bio/Factory/FTLocationFactory.pm \
Bio/Factory/HitFactoryI.pm \
Bio/Factory/LocationFactoryI.pm \
Bio/Factory/MapFactoryI.pm \
Bio/Factory/ObjectBuilderI.pm \
Bio/Factory/ObjectFactory.pm \
Bio/Factory/ObjectFactoryI.pm \
Bio/Factory/ResultFactoryI.pm \
Bio/Factory/SeqAnalysisParserFactory.pm \
Bio/Factory/SeqAnalysisParserFactoryI.pm \
Bio/Factory/SequenceFactoryI.pm \
Bio/Factory/SequenceProcessorI.pm \
Bio/Factory/SequenceStreamI.pm \
Bio/Factory/TreeFactoryI.pm \
Bio/FeatureHolderI.pm \
Bio/Graphics.pm \
Bio/Graphics/Feature.pm \
Bio/Graphics/FeatureFile.pm \
Bio/Graphics/FeatureFile/Iterator.pm \
Bio/Graphics/Glyph.pm \
Bio/Graphics/Glyph/Factory.pm \
Bio/Graphics/Glyph/alignment.pm \
Bio/Graphics/Glyph/anchored_arrow.pm \
Bio/Graphics/Glyph/arrow.pm \
Bio/Graphics/Glyph/box.pm \
Bio/Graphics/Glyph/cds.pm \
Bio/Graphics/Glyph/crossbox.pm \
Bio/Graphics/Glyph/diamond.pm \
Bio/Graphics/Glyph/dna.pm \
Bio/Graphics/Glyph/dot.pm \
Bio/Graphics/Glyph/ellipse.pm \
Bio/Graphics/Glyph/ex.pm \
Bio/Graphics/Glyph/extending_arrow.pm \
Bio/Graphics/Glyph/generic.pm \
Bio/Graphics/Glyph/graded_segments.pm \
Bio/Graphics/Glyph/group.pm \
Bio/Graphics/Glyph/heterogeneous_segments.pm \
Bio/Graphics/Glyph/line.pm \
Bio/Graphics/Glyph/minmax.pm \
Bio/Graphics/Glyph/oval.pm \
Bio/Graphics/Glyph/pinsertion.pm \
Bio/Graphics/Glyph/primers.pm \
Bio/Graphics/Glyph/processed_transcript.pm \
Bio/Graphics/Glyph/redgreen_box.pm \
Bio/Graphics/Glyph/redgreen_segment.pm \
Bio/Graphics/Glyph/rndrect.pm \
Bio/Graphics/Glyph/ruler_arrow.pm \
Bio/Graphics/Glyph/segmented_keyglyph.pm \
Bio/Graphics/Glyph/segments.pm \
Bio/Graphics/Glyph/span.pm \
Bio/Graphics/Glyph/splice_site.pm \
Bio/Graphics/Glyph/toomany.pm \
Bio/Graphics/Glyph/track.pm \
Bio/Graphics/Glyph/transcript.pm \
Bio/Graphics/Glyph/transcript2.pm \
Bio/Graphics/Glyph/translation.pm \
Bio/Graphics/Glyph/triangle.pm \
Bio/Graphics/Glyph/xyplot.pm \
Bio/Graphics/Panel.pm \
Bio/Graphics/Pictogram.pm \
Bio/Graphics/RendererI.pm \
Bio/IdCollectionI.pm \
Bio/IdentifiableI.pm \
Bio/Index/Abstract.pm \
Bio/Index/AbstractSeq.pm \
Bio/Index/Blast.pm \
Bio/Index/EMBL.pm \
Bio/Index/Fasta.pm \
Bio/Index/Fastq.pm \
Bio/Index/GenBank.pm \
Bio/Index/SwissPfam.pm \
Bio/Index/Swissprot.pm \
Bio/LiveSeq/AARange.pm \
Bio/LiveSeq/Chain.pm \
Bio/LiveSeq/ChainI.pm \
Bio/LiveSeq/DNA.pm \
Bio/LiveSeq/Exon.pm \
Bio/LiveSeq/Gene.pm \
Bio/LiveSeq/IO/BioPerl.pm \
Bio/LiveSeq/IO/Loader.pm \
Bio/LiveSeq/IO/SRS.pm \
Bio/LiveSeq/Intron.pm \
Bio/LiveSeq/Mutation.pm \
Bio/LiveSeq/Mutator.pm \
Bio/LiveSeq/Prim_Transcript.pm \
Bio/LiveSeq/Range.pm \
Bio/LiveSeq/Repeat_Region.pm \
Bio/LiveSeq/Repeat_Unit.pm \
Bio/LiveSeq/SeqI.pm \
Bio/LiveSeq/Transcript.pm \
Bio/LiveSeq/Translation.pm \
Bio/LocatableSeq.pm \
Bio/Location/Atomic.pm \
Bio/Location/AvWithinCoordPolicy.pm \
Bio/Location/CoordinatePolicyI.pm \
Bio/Location/Fuzzy.pm \
Bio/Location/FuzzyLocationI.pm \
Bio/Location/NarrowestCoordPolicy.pm \
Bio/Location/Simple.pm \
Bio/Location/Split.pm \
Bio/Location/SplitLocationI.pm \
Bio/Location/WidestCoordPolicy.pm \
Bio/LocationI.pm \
Bio/Map/CytoMap.pm \
Bio/Map/CytoMarker.pm \
Bio/Map/CytoPosition.pm \
Bio/Map/LinkageMap.pm \
Bio/Map/LinkagePosition.pm \
Bio/Map/MapI.pm \
Bio/Map/MappableI.pm \
Bio/Map/Marker.pm \
Bio/Map/MarkerI.pm \
Bio/Map/Microsatellite.pm \
Bio/Map/OrderedPosition.pm \
Bio/Map/OrderedPositionWithDistance.pm \
Bio/Map/Position.pm \
Bio/Map/PositionI.pm \
Bio/Map/SimpleMap.pm \
Bio/MapIO.pm \
Bio/MapIO/mapmaker.pm \
Bio/Matrix/Generic.pm \
Bio/Matrix/IO.pm \
Bio/Matrix/IO/phylip.pm \
Bio/Matrix/IO/scoring.pm \
Bio/Matrix/MatrixI.pm \
Bio/Matrix/PSM/IO.pm \
Bio/Matrix/PSM/IO/mast.pm \
Bio/Matrix/PSM/IO/meme.pm \
Bio/Matrix/PSM/IO/transfac.pm \
Bio/Matrix/PSM/InstanceSite.pm \
Bio/Matrix/PSM/InstanceSiteI.pm \
Bio/Matrix/PSM/Psm.pm \
Bio/Matrix/PSM/PsmHeader.pm \
Bio/Matrix/PSM/PsmHeaderI.pm \
Bio/Matrix/PSM/PsmI.pm \
Bio/Matrix/PSM/SiteMatrix.pm \
Bio/Matrix/PSM/SiteMatrixI.pm \
Bio/Matrix/PhylipDist.pm \
Bio/Matrix/Scoring.pm \
Bio/Ontology/GOterm.pm \
Bio/Ontology/InterProTerm.pm \
Bio/Ontology/Ontology.pm \
Bio/Ontology/OntologyEngineI.pm \
Bio/Ontology/OntologyI.pm \
Bio/Ontology/OntologyStore.pm \
Bio/Ontology/Path.pm \
Bio/Ontology/PathI.pm \
Bio/Ontology/Relationship.pm \
Bio/Ontology/RelationshipFactory.pm \
Bio/Ontology/RelationshipI.pm \
Bio/Ontology/RelationshipType.pm \
Bio/Ontology/SimpleGOEngine.pm \
Bio/Ontology/SimpleOntologyEngine.pm \
Bio/Ontology/Term.pm \
Bio/Ontology/TermFactory.pm \
Bio/Ontology/TermI.pm \
Bio/OntologyIO.pm \
Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
Bio/OntologyIO/Handlers/InterProHandler.pm \
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm \
Bio/OntologyIO/InterProParser.pm \
Bio/OntologyIO/dagflat.pm \
Bio/OntologyIO/goflat.pm \
Bio/OntologyIO/simplehierarchy.pm \
Bio/OntologyIO/soflat.pm \
Bio/Perl.pm \
Bio/Phenotype/Correlate.pm \
Bio/Phenotype/MeSH/Term.pm \
Bio/Phenotype/MeSH/Twig.pm \
Bio/Phenotype/Measure.pm \
Bio/Phenotype/OMIM/MiniMIMentry.pm \
Bio/Phenotype/OMIM/OMIMentry.pm \
Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm \
Bio/Phenotype/OMIM/OMIMparser.pm \
Bio/Phenotype/Phenotype.pm \
Bio/Phenotype/PhenotypeI.pm \
Bio/PopGen/Genotype.pm \
Bio/PopGen/GenotypeI.pm \
Bio/PopGen/IO.pm \
Bio/PopGen/IO/csv.pm \
Bio/PopGen/IO/prettybase.pm \
Bio/PopGen/Individual.pm \
Bio/PopGen/IndividualI.pm \
Bio/PopGen/Marker.pm \
Bio/PopGen/MarkerI.pm \
Bio/PopGen/PopStats.pm \
Bio/PopGen/Population.pm \
Bio/PopGen/PopulationI.pm \
Bio/PopGen/Simulation/Coalescent.pm \
Bio/PopGen/Simulation/GeneticDrift.pm \
Bio/PopGen/Statistics.pm \
Bio/PrimarySeq.pm \
Bio/PrimarySeqI.pm \
Bio/Range.pm \
Bio/RangeI.pm \
Bio/Restriction/Analysis.pm \
Bio/Restriction/Enzyme.pm \
Bio/Restriction/Enzyme/MultiCut.pm \
Bio/Restriction/Enzyme/MultiSite.pm \
Bio/Restriction/EnzymeCollection.pm \
Bio/Restriction/EnzymeI.pm \
Bio/Restriction/IO.pm \
Bio/Restriction/IO/bairoch.pm \
Bio/Restriction/IO/base.pm \
Bio/Restriction/IO/itype2.pm \
Bio/Restriction/IO/withrefm.pm \
Bio/Root/Err.pm \
Bio/Root/Exception.pm \
Bio/Root/Global.pm \
Bio/Root/HTTPget.pm \
Bio/Root/IO.pm \
Bio/Root/IOManager.pm \
Bio/Root/Object.pm \
Bio/Root/Root.pm \
Bio/Root/RootI.pm \
Bio/Root/Storable.pm \
Bio/Root/Utilities.pm \
Bio/Root/Vector.pm \
Bio/Root/Version.pm \
Bio/Root/Xref.pm \
Bio/Search/BlastUtils.pm \
Bio/Search/DatabaseI.pm \
Bio/Search/GenericDatabase.pm \
Bio/Search/HSP/BlastHSP.pm \
Bio/Search/HSP/FastaHSP.pm \
Bio/Search/HSP/GenericHSP.pm \
Bio/Search/HSP/HMMERHSP.pm \
Bio/Search/HSP/HSPFactory.pm \
Bio/Search/HSP/HSPI.pm \
Bio/Search/HSP/PSLHSP.pm \
Bio/Search/HSP/PsiBlastHSP.pm \
Bio/Search/HSP/WABAHSP.pm \
Bio/Search/Hit/BlastHit.pm \
Bio/Search/Hit/Fasta.pm \
Bio/Search/Hit/GenericHit.pm \
Bio/Search/Hit/HMMERHit.pm \
Bio/Search/Hit/HitFactory.pm \
Bio/Search/Hit/HitI.pm \
Bio/Search/Hit/PsiBlastHit.pm \
Bio/Search/Iteration/GenericIteration.pm \
Bio/Search/Iteration/IterationI.pm \
Bio/Search/Processor.pm \
Bio/Search/Result/BlastResult.pm \
Bio/Search/Result/GenericResult.pm \
Bio/Search/Result/HMMERResult.pm \
Bio/Search/Result/ResultFactory.pm \
Bio/Search/Result/ResultI.pm \
Bio/Search/Result/WABAResult.pm \
Bio/Search/SearchUtils.pm \
Bio/SearchDist.pm \
Bio/SearchIO.pm \
Bio/SearchIO/EventHandlerI.pm \
Bio/SearchIO/FastHitEventBuilder.pm \
Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
Bio/SearchIO/SearchResultEventBuilder.pm \
Bio/SearchIO/SearchWriterI.pm \
Bio/SearchIO/Writer/BSMLResultWriter.pm \
Bio/SearchIO/Writer/GbrowseGFF.pm \
Bio/SearchIO/Writer/HSPTableWriter.pm \
Bio/SearchIO/Writer/HTMLResultWriter.pm \
Bio/SearchIO/Writer/HitTableWriter.pm \
Bio/SearchIO/Writer/ResultTableWriter.pm \
Bio/SearchIO/Writer/TextResultWriter.pm \
Bio/SearchIO/axt.pm \
Bio/SearchIO/blast.pm \
Bio/SearchIO/blasttable.pm \
Bio/SearchIO/blastxml.pm \
Bio/SearchIO/exonerate.pm \
Bio/SearchIO/fasta.pm \
Bio/SearchIO/hmmer.pm \
Bio/SearchIO/megablast.pm \
Bio/SearchIO/psl.pm \
Bio/SearchIO/sim4.pm \
Bio/SearchIO/waba.pm \
Bio/SearchIO/wise.pm \
Bio/Seq.pm \
Bio/Seq/BaseSeqProcessor.pm \
Bio/Seq/EncodedSeq.pm \
Bio/Seq/LargePrimarySeq.pm \
Bio/Seq/LargeSeq.pm \
Bio/Seq/Meta.pm \
Bio/Seq/Meta/Array.pm \
Bio/Seq/MetaI.pm \
Bio/Seq/PrimaryQual.pm \
Bio/Seq/PrimedSeq.pm \
Bio/Seq/QualI.pm \
Bio/Seq/RichSeq.pm \
Bio/Seq/RichSeqI.pm \
Bio/Seq/SeqBuilder.pm \
Bio/Seq/SeqFactory.pm \
Bio/Seq/SeqFastaSpeedFactory.pm \
Bio/Seq/SeqWithQuality.pm \
Bio/Seq/SequenceTrace.pm \
Bio/Seq/TraceI.pm \
Bio/SeqAnalysisParserI.pm \
Bio/SeqFeature/AnnotationAdaptor.pm \
Bio/SeqFeature/Collection.pm \
Bio/SeqFeature/CollectionI.pm \
Bio/SeqFeature/Computation.pm \
Bio/SeqFeature/FeaturePair.pm \
Bio/SeqFeature/Gene/Exon.pm \
Bio/SeqFeature/Gene/ExonI.pm \
Bio/SeqFeature/Gene/GeneStructure.pm \
Bio/SeqFeature/Gene/GeneStructureI.pm \
Bio/SeqFeature/Gene/Intron.pm \
Bio/SeqFeature/Gene/NC_Feature.pm \
Bio/SeqFeature/Gene/Poly_A_site.pm \
Bio/SeqFeature/Gene/Promoter.pm \
Bio/SeqFeature/Gene/Transcript.pm \
Bio/SeqFeature/Gene/TranscriptI.pm \
Bio/SeqFeature/Gene/UTR.pm \
Bio/SeqFeature/Generic.pm \
Bio/SeqFeature/PositionProxy.pm \
Bio/SeqFeature/Primer.pm \
Bio/SeqFeature/SiRNA/Oligo.pm \
Bio/SeqFeature/SiRNA/Pair.pm \
Bio/SeqFeature/Similarity.pm \
Bio/SeqFeature/SimilarityPair.pm \
Bio/SeqFeature/Tools/TypeMapper.pm \
Bio/SeqFeature/Tools/Unflattener.pm \
Bio/SeqFeatureI.pm \
Bio/SeqI.pm \
Bio/SeqIO.pm \
Bio/SeqIO/FTHelper.pm \
Bio/SeqIO/MultiFile.pm \
Bio/SeqIO/abi.pm \
Bio/SeqIO/ace.pm \
Bio/SeqIO/alf.pm \
Bio/SeqIO/asciitree.pm \
Bio/SeqIO/bsml.pm \
Bio/SeqIO/chadoxml.pm \
Bio/SeqIO/ctf.pm \
Bio/SeqIO/embl.pm \
Bio/SeqIO/exp.pm \
Bio/SeqIO/fasta.pm \
Bio/SeqIO/fastq.pm \
Bio/SeqIO/game.pm \
Bio/SeqIO/game/featHandler.pm \
Bio/SeqIO/game/gameHandler.pm \
Bio/SeqIO/game/gameSubs.pm \
Bio/SeqIO/game/gameWriter.pm \
Bio/SeqIO/game/seqHandler.pm \
Bio/SeqIO/gcg.pm \
Bio/SeqIO/genbank.pm \
Bio/SeqIO/kegg.pm \
Bio/SeqIO/largefasta.pm \
Bio/SeqIO/locuslink.pm \
Bio/SeqIO/metafasta.pm \
Bio/SeqIO/phd.pm \
Bio/SeqIO/pir.pm \
Bio/SeqIO/pln.pm \
Bio/SeqIO/qual.pm \
Bio/SeqIO/raw.pm \
Bio/SeqIO/scf.pm \
Bio/SeqIO/swiss.pm \
Bio/SeqIO/tab.pm \
Bio/SeqIO/tigr.pm \
Bio/SeqIO/ztr.pm \
Bio/SeqUtils.pm \
Bio/SimpleAlign.pm \
Bio/SimpleAnalysisI.pm \
Bio/Species.pm \
Bio/Structure/Atom.pm \
Bio/Structure/Chain.pm \
Bio/Structure/Entry.pm \
Bio/Structure/IO.pm \
Bio/Structure/IO/pdb.pm \
Bio/Structure/Model.pm \
Bio/Structure/Residue.pm \
Bio/Structure/SecStr/DSSP/Res.pm \
Bio/Structure/SecStr/STRIDE/Res.pm \
Bio/Structure/StructureI.pm \
Bio/Symbol/Alphabet.pm \
Bio/Symbol/AlphabetI.pm \
Bio/Symbol/DNAAlphabet.pm \
Bio/Symbol/ProteinAlphabet.pm \
Bio/Symbol/Symbol.pm \
Bio/Symbol/SymbolI.pm \
Bio/Taxonomy.pm \
Bio/Taxonomy/FactoryI.pm \
Bio/Taxonomy/Node.pm \
Bio/Taxonomy/Taxon.pm \
Bio/Taxonomy/Tree.pm \
Bio/Tools/AlignFactory.pm \
Bio/Tools/Alignment/Consed.pm \
Bio/Tools/Alignment/Trim.pm \
Bio/Tools/Analysis/DNA/ESEfinder.pm \
Bio/Tools/Analysis/Protein/Domcut.pm \
Bio/Tools/Analysis/Protein/ELM.pm \
Bio/Tools/Analysis/Protein/GOR4.pm \
Bio/Tools/Analysis/Protein/HNN.pm \
Bio/Tools/Analysis/Protein/Mitoprot.pm \
Bio/Tools/Analysis/Protein/NetPhos.pm \
Bio/Tools/Analysis/Protein/Scansite.pm \
Bio/Tools/Analysis/Protein/Sopma.pm \
Bio/Tools/Analysis/SimpleAnalysisBase.pm \
Bio/Tools/AnalysisResult.pm \
Bio/Tools/BPbl2seq.pm \
Bio/Tools/BPlite.pm \
Bio/Tools/BPlite/HSP.pm \
Bio/Tools/BPlite/Iteration.pm \
Bio/Tools/BPlite/Sbjct.pm \
Bio/Tools/BPpsilite.pm \
Bio/Tools/Blast.pm \
Bio/Tools/Blast/HSP.pm \
Bio/Tools/Blast/HTML.pm \
Bio/Tools/Blast/Sbjct.pm \
Bio/Tools/Blat.pm \
Bio/Tools/CodonTable.pm \
Bio/Tools/Coil.pm \
Bio/Tools/ECnumber.pm \
Bio/Tools/EMBOSS/Palindrome.pm \
Bio/Tools/EPCR.pm \
Bio/Tools/ESTScan.pm \
Bio/Tools/Eponine.pm \
Bio/Tools/Est2Genome.pm \
Bio/Tools/FootPrinter.pm \
Bio/Tools/GFF.pm \
Bio/Tools/Gel.pm \
Bio/Tools/Geneid.pm \
Bio/Tools/Genemark.pm \
Bio/Tools/Genewise.pm \
Bio/Tools/Genomewise.pm \
Bio/Tools/Genscan.pm \
Bio/Tools/Glimmer.pm \
Bio/Tools/Grail.pm \
Bio/Tools/GuessSeqFormat.pm \
Bio/Tools/HMMER/Domain.pm \
Bio/Tools/HMMER/Results.pm \
Bio/Tools/HMMER/Set.pm \
Bio/Tools/Hmmpfam.pm \
Bio/Tools/IUPAC.pm \
Bio/Tools/Lucy.pm \
Bio/Tools/MZEF.pm \
Bio/Tools/OddCodes.pm \
Bio/Tools/Phylo/Molphy.pm \
Bio/Tools/Phylo/Molphy/Result.pm \
Bio/Tools/Phylo/PAML.pm \
Bio/Tools/Phylo/PAML/ModelResult.pm \
Bio/Tools/Phylo/PAML/Result.pm \
Bio/Tools/Phylo/Phylip/ProtDist.pm \
Bio/Tools/Prediction/Exon.pm \
Bio/Tools/Prediction/Gene.pm \
Bio/Tools/Primer/Assessor/Base.pm \
Bio/Tools/Primer/AssessorI.pm \
Bio/Tools/Primer/Feature.pm \
Bio/Tools/Primer/Pair.pm \
Bio/Tools/Primer3.pm \
Bio/Tools/Prints.pm \
Bio/Tools/Profile.pm \
Bio/Tools/Promoterwise.pm \
Bio/Tools/PrositeScan.pm \
Bio/Tools/Pseudowise.pm \
Bio/Tools/QRNA.pm \
Bio/Tools/RandomDistFunctions.pm \
Bio/Tools/RepeatMasker.pm \
Bio/Tools/RestrictionEnzyme.pm \
Bio/Tools/Run/RemoteBlast.pm \
Bio/Tools/Run/StandAloneBlast.pm \
Bio/Tools/Run/WrapperBase.pm \
Bio/Tools/Seg.pm \
Bio/Tools/SeqAnal.pm \
Bio/Tools/SeqPattern.pm \
Bio/Tools/SeqStats.pm \
Bio/Tools/SeqWords.pm \
Bio/Tools/SiRNA.pm \
Bio/Tools/Sigcleave.pm \
Bio/Tools/Signalp.pm \
Bio/Tools/Sim4/Exon.pm \
Bio/Tools/Sim4/Results.pm \
Bio/Tools/Tmhmm.pm \
Bio/Tools/WWW.pm \
Bio/Tools/dpAlign.pm \
Bio/Tools/pICalculator.pm \
Bio/Tools/pSW.pm \
Bio/Tree/AlleleNode.pm \
Bio/Tree/Node.pm \
Bio/Tree/NodeI.pm \
Bio/Tree/NodeNHX.pm \
Bio/Tree/RandomFactory.pm \
Bio/Tree/Statistics.pm \
Bio/Tree/Tree.pm \
Bio/Tree/TreeFunctionsI.pm \
Bio/Tree/TreeI.pm \
Bio/TreeIO.pm \
Bio/TreeIO/TreeEventBuilder.pm \
Bio/TreeIO/lintree.pm \
Bio/TreeIO/newick.pm \
Bio/TreeIO/nexus.pm \
Bio/TreeIO/nhx.pm \
Bio/TreeIO/svggraph.pm \
Bio/TreeIO/tabtree.pm \
Bio/UpdateableSeqI.pm \
Bio/Variation/AAChange.pm \
Bio/Variation/AAReverseMutate.pm \
Bio/Variation/Allele.pm \
Bio/Variation/DNAMutation.pm \
Bio/Variation/IO.pm \
Bio/Variation/IO/flat.pm \
Bio/Variation/IO/xml.pm \
Bio/Variation/RNAChange.pm \
Bio/Variation/SNP.pm \
Bio/Variation/SeqDiff.pm \
Bio/Variation/VariantI.pm \
Bio/WebAgent.pm \
biodatabases.pod \
biodesign.pod \
bioperl.pod \
bioscripts.pod \
bptutorial.pl
HTMLEXT = html
INST_MAN1DIR = blib/man1
INSTALLMAN1DIR = /usr/share/doclib/annex/man/man1
MAN1EXT = 1
INST_MAN3DIR = blib/man3
INSTALLMAN3DIR = /usr/share/doclib/annex/man/man3
MAN3EXT = 3
PERM_RW = 644
PERM_RWX = 755
# work around a famous dec-osf make(1) feature(?):
makemakerdflt: all
.SUFFIXES: .xs .c .C .cpp .cxx .cc $(OBJ_EXT)
# Nick wanted to get rid of .PRECIOUS. I don't remember why. I seem to recall, that
# some make implementations will delete the Makefile when we rebuild it. Because
# we call false(1) when we rebuild it. So make(1) is not completely wrong when it
# does so. Our milage may vary.
# .PRECIOUS: Makefile # seems to be not necessary anymore
.PHONY: all config static dynamic test linkext manifest
# Where is the Config information that we are using/depend on
CONFIGDEP = $(PERL_ARCHLIB)/Config.pm $(PERL_INC)/config.h
# Where to put things:
INST_LIBDIR = $(INST_LIB)
INST_ARCHLIBDIR = $(INST_ARCHLIB)
INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
INST_STATIC =
INST_DYNAMIC =
INST_BOOT =
EXPORT_LIST =
PERL_ARCHIVE =
TO_INST_PM = Bio/Align/AlignI.pm \
Bio/Align/DNAStatistics.pm \
Bio/Align/PairwiseStatistics.pm \
Bio/Align/StatisticsI.pm \
Bio/Align/Utilities.pm \
Bio/AlignIO.pm \
Bio/AlignIO/bl2seq.pm \
Bio/AlignIO/clustalw.pm \
Bio/AlignIO/emboss.pm \
Bio/AlignIO/fasta.pm \
Bio/AlignIO/maf.pm \
Bio/AlignIO/mase.pm \
Bio/AlignIO/mega.pm \
Bio/AlignIO/meme.pm \
Bio/AlignIO/metafasta.pm \
Bio/AlignIO/msf.pm \
Bio/AlignIO/nexus.pm \
Bio/AlignIO/pfam.pm \
Bio/AlignIO/phylip.pm \
Bio/AlignIO/prodom.pm \
Bio/AlignIO/psi.pm \
Bio/AlignIO/selex.pm \
Bio/AlignIO/stockholm.pm \
Bio/AnalysisI.pm \
Bio/AnalysisParserI.pm \
Bio/AnalysisResultI.pm \
Bio/AnnotatableI.pm \
Bio/Annotation/AnnotationFactory.pm \
Bio/Annotation/Collection.pm \
Bio/Annotation/Comment.pm \
Bio/Annotation/DBLink.pm \
Bio/Annotation/OntologyTerm.pm \
Bio/Annotation/Reference.pm \
Bio/Annotation/SimpleValue.pm \
Bio/Annotation/StructuredValue.pm \
Bio/Annotation/TypeManager.pm \
Bio/AnnotationCollectionI.pm \
Bio/AnnotationI.pm \
Bio/Assembly/Contig.pm \
Bio/Assembly/ContigAnalysis.pm \
Bio/Assembly/IO.pm \
Bio/Assembly/IO/ace.pm \
Bio/Assembly/IO/phrap.pm \
Bio/Assembly/Scaffold.pm \
Bio/Assembly/ScaffoldI.pm \
Bio/Biblio.pm \
Bio/Biblio/Article.pm \
Bio/Biblio/BiblioBase.pm \
Bio/Biblio/Book.pm \
Bio/Biblio/BookArticle.pm \
Bio/Biblio/IO.pm \
Bio/Biblio/IO/medline2ref.pm \
Bio/Biblio/IO/medlinexml.pm \
Bio/Biblio/IO/pubmed2ref.pm \
Bio/Biblio/IO/pubmedxml.pm \
Bio/Biblio/Journal.pm \
Bio/Biblio/JournalArticle.pm \
Bio/Biblio/MedlineArticle.pm \
Bio/Biblio/MedlineBook.pm \
Bio/Biblio/MedlineBookArticle.pm \
Bio/Biblio/MedlineJournal.pm \
Bio/Biblio/MedlineJournalArticle.pm \
Bio/Biblio/Organisation.pm \
Bio/Biblio/Patent.pm \
Bio/Biblio/Person.pm \
Bio/Biblio/Proceeding.pm \
Bio/Biblio/Provider.pm \
Bio/Biblio/PubmedArticle.pm \
Bio/Biblio/PubmedBookArticle.pm \
Bio/Biblio/PubmedJournalArticle.pm \
Bio/Biblio/Ref.pm \
Bio/Biblio/Service.pm \
Bio/Biblio/TechReport.pm \
Bio/Biblio/Thesis.pm \
Bio/Biblio/WebResource.pm \
Bio/Cluster/ClusterFactory.pm \
Bio/Cluster/FamilyI.pm \
Bio/Cluster/SequenceFamily.pm \
Bio/Cluster/UniGene.pm \
Bio/Cluster/UniGeneI.pm \
Bio/ClusterI.pm \
Bio/ClusterIO.pm \
Bio/ClusterIO/dbsnp.pm \
Bio/ClusterIO/unigene.pm \
Bio/CodonUsage/IO.pm \
Bio/CodonUsage/Table.pm \
Bio/Coordinate/Chain.pm \
Bio/Coordinate/Collection.pm \
Bio/Coordinate/ExtrapolatingPair.pm \
Bio/Coordinate/GeneMapper.pm \
Bio/Coordinate/Graph.pm \
Bio/Coordinate/MapperI.pm \
Bio/Coordinate/Pair.pm \
Bio/Coordinate/Result.pm \
Bio/Coordinate/Result/Gap.pm \
Bio/Coordinate/Result/Match.pm \
Bio/Coordinate/ResultI.pm \
Bio/Coordinate/Utils.pm \
Bio/DB/Ace.pm \
Bio/DB/Biblio/biofetch.pm \
Bio/DB/Biblio/soap.pm \
Bio/DB/BiblioI.pm \
Bio/DB/BioFetch.pm \
Bio/DB/CUTG.pm \
Bio/DB/DBFetch.pm \
Bio/DB/EMBL.pm \
Bio/DB/Failover.pm \
Bio/DB/Fasta.pm \
Bio/DB/FileCache.pm \
Bio/DB/Flat.pm \
Bio/DB/Flat/BDB.pm \
Bio/DB/Flat/BDB/embl.pm \
Bio/DB/Flat/BDB/fasta.pm \
Bio/DB/Flat/BDB/genbank.pm \
Bio/DB/Flat/BDB/swiss.pm \
Bio/DB/Flat/BDB/swissprot.pm \
Bio/DB/Flat/BinarySearch.pm \
Bio/DB/GDB.pm \
Bio/DB/GFF.pm \
Bio/DB/GFF/Adaptor/ace.pm \
Bio/DB/GFF/Adaptor/biofetch.pm \
Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
Bio/DB/GFF/Adaptor/dbi.pm \
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
Bio/DB/GFF/Adaptor/dbi/iterator.pm \
Bio/DB/GFF/Adaptor/dbi/mysql.pm \
Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
Bio/DB/GFF/Adaptor/dbi/oracle.pm \
Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
Bio/DB/GFF/Adaptor/dbi/pg.pm \
Bio/DB/GFF/Adaptor/memory.pm \
Bio/DB/GFF/Adaptor/memory_iterator.pm \
Bio/DB/GFF/Aggregator.pm \
Bio/DB/GFF/Aggregator/alignment.pm \
Bio/DB/GFF/Aggregator/clone.pm \
Bio/DB/GFF/Aggregator/coding.pm \
Bio/DB/GFF/Aggregator/match.pm \
Bio/DB/GFF/Aggregator/none.pm \
Bio/DB/GFF/Aggregator/processed_transcript.pm \
Bio/DB/GFF/Aggregator/transcript.pm \
Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
Bio/DB/GFF/Featname.pm \
Bio/DB/GFF/Feature.pm \
Bio/DB/GFF/Homol.pm \
Bio/DB/GFF/RelSegment.pm \
Bio/DB/GFF/Segment.pm \
Bio/DB/GFF/Typename.pm \
Bio/DB/GFF/Util/Binning.pm \
Bio/DB/GFF/Util/Rearrange.pm \
Bio/DB/GenBank.pm \
Bio/DB/GenPept.pm \
Bio/DB/InMemoryCache.pm \
Bio/DB/MANIFEST \
Bio/DB/Makefile.PL \
Bio/DB/MeSH.pm \
Bio/DB/NCBIHelper.pm \
Bio/DB/Query/GenBank.pm \
Bio/DB/Query/WebQuery.pm \
Bio/DB/QueryI.pm \
Bio/DB/RandomAccessI.pm \
Bio/DB/RefSeq.pm \
Bio/DB/Registry.pm \
Bio/DB/SeqI.pm \
Bio/DB/SwissProt.pm \
Bio/DB/Taxonomy.pm \
Bio/DB/Taxonomy/entrez.pm \
Bio/DB/Taxonomy/flatfile.pm \
Bio/DB/Universal.pm \
Bio/DB/UpdateableSeqI.pm \
Bio/DB/WebDBSeqI.pm \
Bio/DB/XEMBL.pm \
Bio/DB/XEMBLService.pm \
Bio/DBLinkContainerI.pm \
Bio/Das/FeatureTypeI.pm \
Bio/Das/SegmentI.pm \
Bio/DasI.pm \
Bio/DescribableI.pm \
Bio/Event/EventGeneratorI.pm \
Bio/Event/EventHandlerI.pm \
Bio/Expression/FeatureGroup.pm \
Bio/Expression/FeatureGroup/FeatureGroupMas50.pm \
Bio/Expression/FeatureI.pm \
Bio/Expression/FeatureSet/FeatureSetMas50.pm \
Bio/Factory/AnalysisI.pm \
Bio/Factory/ApplicationFactoryI.pm \
Bio/Factory/DriverFactory.pm \
Bio/Factory/FTLocationFactory.pm \
Bio/Factory/HitFactoryI.pm \
Bio/Factory/LocationFactoryI.pm \
Bio/Factory/MapFactoryI.pm \
Bio/Factory/ObjectBuilderI.pm \
Bio/Factory/ObjectFactory.pm \
Bio/Factory/ObjectFactoryI.pm \
Bio/Factory/ResultFactoryI.pm \
Bio/Factory/SeqAnalysisParserFactory.pm \
Bio/Factory/SeqAnalysisParserFactoryI.pm \
Bio/Factory/SequenceFactoryI.pm \
Bio/Factory/SequenceProcessorI.pm \
Bio/Factory/SequenceStreamI.pm \
Bio/Factory/TreeFactoryI.pm \
Bio/FeatureHolderI.pm \
Bio/Graphics.pm \
Bio/Graphics/ConfiguratorI.pm \
Bio/Graphics/Feature.pm \
Bio/Graphics/FeatureFile.pm \
Bio/Graphics/FeatureFile/Iterator.pm \
Bio/Graphics/Glyph.pm \
Bio/Graphics/Glyph/Factory.pm \
Bio/Graphics/Glyph/alignment.pm \
Bio/Graphics/Glyph/anchored_arrow.pm \
Bio/Graphics/Glyph/arrow.pm \
Bio/Graphics/Glyph/box.pm \
Bio/Graphics/Glyph/cds.pm \
Bio/Graphics/Glyph/crossbox.pm \
Bio/Graphics/Glyph/diamond.pm \
Bio/Graphics/Glyph/dna.pm \
Bio/Graphics/Glyph/dot.pm \
Bio/Graphics/Glyph/ellipse.pm \
Bio/Graphics/Glyph/ex.pm \
Bio/Graphics/Glyph/extending_arrow.pm \
Bio/Graphics/Glyph/generic.pm \
Bio/Graphics/Glyph/graded_segments.pm \
Bio/Graphics/Glyph/group.pm \
Bio/Graphics/Glyph/heterogeneous_segments.pm \
Bio/Graphics/Glyph/line.pm \
Bio/Graphics/Glyph/minmax.pm \
Bio/Graphics/Glyph/oval.pm \
Bio/Graphics/Glyph/pinsertion.pm \
Bio/Graphics/Glyph/primers.pm \
Bio/Graphics/Glyph/processed_transcript.pm \
Bio/Graphics/Glyph/redgreen_box.pm \
Bio/Graphics/Glyph/redgreen_segment.pm \
Bio/Graphics/Glyph/rndrect.pm \
Bio/Graphics/Glyph/ruler_arrow.pm \
Bio/Graphics/Glyph/segmented_keyglyph.pm \
Bio/Graphics/Glyph/segments.pm \
Bio/Graphics/Glyph/span.pm \
Bio/Graphics/Glyph/splice_site.pm \
Bio/Graphics/Glyph/toomany.pm \
Bio/Graphics/Glyph/track.pm \
Bio/Graphics/Glyph/transcript.pm \
Bio/Graphics/Glyph/transcript2.pm \
Bio/Graphics/Glyph/translation.pm \
Bio/Graphics/Glyph/triangle.pm \
Bio/Graphics/Glyph/xyplot.pm \
Bio/Graphics/Panel.pm \
Bio/Graphics/Pictogram.pm \
Bio/Graphics/RendererI.pm \
Bio/Graphics/Util.pm \
Bio/IdCollectionI.pm \
Bio/IdentifiableI.pm \
Bio/Index/Abstract.pm \
Bio/Index/AbstractSeq.pm \
Bio/Index/Blast.pm \
Bio/Index/EMBL.pm \
Bio/Index/Fasta.pm \
Bio/Index/Fastq.pm \
Bio/Index/GenBank.pm \
Bio/Index/SwissPfam.pm \
Bio/Index/Swissprot.pm \
Bio/LiveSeq/AARange.pm \
Bio/LiveSeq/Chain.pm \
Bio/LiveSeq/ChainI.pm \
Bio/LiveSeq/DNA.pm \
Bio/LiveSeq/Exon.pm \
Bio/LiveSeq/Gene.pm \
Bio/LiveSeq/IO/BioPerl.pm \
Bio/LiveSeq/IO/Loader.pm \
Bio/LiveSeq/IO/README \
Bio/LiveSeq/IO/SRS.pm \
Bio/LiveSeq/Intron.pm \
Bio/LiveSeq/Mutation.pm \
Bio/LiveSeq/Mutator.pm \
Bio/LiveSeq/Prim_Transcript.pm \
Bio/LiveSeq/Range.pm \
Bio/LiveSeq/Repeat_Region.pm \
Bio/LiveSeq/Repeat_Unit.pm \
Bio/LiveSeq/SeqI.pm \
Bio/LiveSeq/Transcript.pm \
Bio/LiveSeq/Translation.pm \
Bio/LocatableSeq.pm \
Bio/Location/Atomic.pm \
Bio/Location/AvWithinCoordPolicy.pm \
Bio/Location/CoordinatePolicyI.pm \
Bio/Location/Fuzzy.pm \
Bio/Location/FuzzyLocationI.pm \
Bio/Location/NarrowestCoordPolicy.pm \
Bio/Location/Simple.pm \
Bio/Location/Split.pm \
Bio/Location/SplitLocationI.pm \
Bio/Location/WidestCoordPolicy.pm \
Bio/LocationI.pm \
Bio/Map/CytoMap.pm \
Bio/Map/CytoMarker.pm \
Bio/Map/CytoPosition.pm \
Bio/Map/LinkageMap.pm \
Bio/Map/LinkagePosition.pm \
Bio/Map/MapI.pm \
Bio/Map/MappableI.pm \
Bio/Map/Marker.pm \
Bio/Map/MarkerI.pm \
Bio/Map/Microsatellite.pm \
Bio/Map/OrderedPosition.pm \
Bio/Map/OrderedPositionWithDistance.pm \
Bio/Map/Position.pm \
Bio/Map/PositionI.pm \
Bio/Map/SimpleMap.pm \
Bio/MapIO.pm \
Bio/MapIO/mapmaker.pm \
Bio/Matrix/Generic.pm \
Bio/Matrix/IO.pm \
Bio/Matrix/IO/phylip.pm \
Bio/Matrix/IO/scoring.pm \
Bio/Matrix/MatrixI.pm \
Bio/Matrix/PSM/IO.pm \
Bio/Matrix/PSM/IO/mast.pm \
Bio/Matrix/PSM/IO/meme.pm \
Bio/Matrix/PSM/IO/transfac.pm \
Bio/Matrix/PSM/InstanceSite.pm \
Bio/Matrix/PSM/InstanceSiteI.pm \
Bio/Matrix/PSM/Psm.pm \
Bio/Matrix/PSM/PsmHeader.pm \
Bio/Matrix/PSM/PsmHeaderI.pm \
Bio/Matrix/PSM/PsmI.pm \
Bio/Matrix/PSM/SiteMatrix.pm \
Bio/Matrix/PSM/SiteMatrixI.pm \
Bio/Matrix/PhylipDist.pm \
Bio/Matrix/Scoring.pm \
Bio/Ontology/GOterm.pm \
Bio/Ontology/InterProTerm.pm \
Bio/Ontology/Ontology.pm \
Bio/Ontology/OntologyEngineI.pm \
Bio/Ontology/OntologyI.pm \
Bio/Ontology/OntologyStore.pm \
Bio/Ontology/Path.pm \
Bio/Ontology/PathI.pm \
Bio/Ontology/Relationship.pm \
Bio/Ontology/RelationshipFactory.pm \
Bio/Ontology/RelationshipI.pm \
Bio/Ontology/RelationshipType.pm \
Bio/Ontology/SimpleGOEngine.pm \
Bio/Ontology/SimpleOntologyEngine.pm \
Bio/Ontology/Term.pm \
Bio/Ontology/TermFactory.pm \
Bio/Ontology/TermI.pm \
Bio/OntologyIO.pm \
Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
Bio/OntologyIO/Handlers/InterProHandler.pm \
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm \
Bio/OntologyIO/InterProParser.pm \
Bio/OntologyIO/dagflat.pm \
Bio/OntologyIO/goflat.pm \
Bio/OntologyIO/simplehierarchy.pm \
Bio/OntologyIO/soflat.pm \
Bio/Perl.pm \
Bio/Phenotype/Correlate.pm \
Bio/Phenotype/MeSH/Term.pm \
Bio/Phenotype/MeSH/Twig.pm \
Bio/Phenotype/Measure.pm \
Bio/Phenotype/OMIM/MiniMIMentry.pm \
Bio/Phenotype/OMIM/OMIMentry.pm \
Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm \
Bio/Phenotype/OMIM/OMIMparser.pm \
Bio/Phenotype/Phenotype.pm \
Bio/Phenotype/PhenotypeI.pm \
Bio/PopGen/Genotype.pm \
Bio/PopGen/GenotypeI.pm \
Bio/PopGen/IO.pm \
Bio/PopGen/IO/csv.pm \
Bio/PopGen/IO/prettybase.pm \
Bio/PopGen/Individual.pm \
Bio/PopGen/IndividualI.pm \
Bio/PopGen/Marker.pm \
Bio/PopGen/MarkerI.pm \
Bio/PopGen/PopStats.pm \
Bio/PopGen/Population.pm \
Bio/PopGen/PopulationI.pm \
Bio/PopGen/Simulation/Coalescent.pm \
Bio/PopGen/Simulation/GeneticDrift.pm \
Bio/PopGen/Statistics.pm \
Bio/PrimarySeq.pm \
Bio/PrimarySeqI.pm \
Bio/Range.pm \
Bio/RangeI.pm \
Bio/Restriction/Analysis.pm \
Bio/Restriction/Enzyme.pm \
Bio/Restriction/Enzyme/MultiCut.pm \
Bio/Restriction/Enzyme/MultiSite.pm \
Bio/Restriction/EnzymeCollection.pm \
Bio/Restriction/EnzymeI.pm \
Bio/Restriction/IO.pm \
Bio/Restriction/IO/bairoch.pm \
Bio/Restriction/IO/base.pm \
Bio/Restriction/IO/itype2.pm \
Bio/Restriction/IO/withrefm.pm \
Bio/Root/Err.pm \
Bio/Root/Exception.pm \
Bio/Root/Global.pm \
Bio/Root/HTTPget.pm \
Bio/Root/IO.pm \
Bio/Root/IOManager.pm \
Bio/Root/Object.pm \
Bio/Root/Root.pm \
Bio/Root/RootI.pm \
Bio/Root/Storable.pm \
Bio/Root/Utilities.pm \
Bio/Root/Vector.pm \
Bio/Root/Version.pm \
Bio/Root/Xref.pm \
Bio/Search/BlastUtils.pm \
Bio/Search/DatabaseI.pm \
Bio/Search/GenericDatabase.pm \
Bio/Search/HSP/BlastHSP.pm \
Bio/Search/HSP/FastaHSP.pm \
Bio/Search/HSP/GenericHSP.pm \
Bio/Search/HSP/HMMERHSP.pm \
Bio/Search/HSP/HSPFactory.pm \
Bio/Search/HSP/HSPI.pm \
Bio/Search/HSP/PSLHSP.pm \
Bio/Search/HSP/PsiBlastHSP.pm \
Bio/Search/HSP/WABAHSP.pm \
Bio/Search/Hit/BlastHit.pm \
Bio/Search/Hit/Fasta.pm \
Bio/Search/Hit/GenericHit.pm \
Bio/Search/Hit/HMMERHit.pm \
Bio/Search/Hit/HitFactory.pm \
Bio/Search/Hit/HitI.pm \
Bio/Search/Hit/PsiBlastHit.pm \
Bio/Search/Iteration/GenericIteration.pm \
Bio/Search/Iteration/IterationI.pm \
Bio/Search/Processor.pm \
Bio/Search/Result/BlastResult.pm \
Bio/Search/Result/GenericResult.pm \
Bio/Search/Result/HMMERResult.pm \
Bio/Search/Result/ResultFactory.pm \
Bio/Search/Result/ResultI.pm \
Bio/Search/Result/WABAResult.pm \
Bio/Search/SearchUtils.pm \
Bio/SearchDist.pm \
Bio/SearchIO.pm \
Bio/SearchIO/EventHandlerI.pm \
Bio/SearchIO/FastHitEventBuilder.pm \
Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
Bio/SearchIO/SearchResultEventBuilder.pm \
Bio/SearchIO/SearchWriterI.pm \
Bio/SearchIO/Writer/BSMLResultWriter.pm \
Bio/SearchIO/Writer/GbrowseGFF.pm \
Bio/SearchIO/Writer/HSPTableWriter.pm \
Bio/SearchIO/Writer/HTMLResultWriter.pm \
Bio/SearchIO/Writer/HitTableWriter.pm \
Bio/SearchIO/Writer/ResultTableWriter.pm \
Bio/SearchIO/Writer/TextResultWriter.pm \
Bio/SearchIO/axt.pm \
Bio/SearchIO/blast.pm \
Bio/SearchIO/blasttable.pm \
Bio/SearchIO/blastxml.pm \
Bio/SearchIO/exonerate.pm \
Bio/SearchIO/fasta.pm \
Bio/SearchIO/hmmer.pm \
Bio/SearchIO/megablast.pm \
Bio/SearchIO/psl.pm \
Bio/SearchIO/sim4.pm \
Bio/SearchIO/waba.pm \
Bio/SearchIO/wise.pm \
Bio/Seq.pm \
Bio/Seq/BaseSeqProcessor.pm \
Bio/Seq/EncodedSeq.pm \
Bio/Seq/LargePrimarySeq.pm \
Bio/Seq/LargeSeq.pm \
Bio/Seq/Meta.pm \
Bio/Seq/Meta/Array.pm \
Bio/Seq/MetaI.pm \
Bio/Seq/PrimaryQual.pm \
Bio/Seq/PrimedSeq.pm \
Bio/Seq/QualI.pm \
Bio/Seq/RichSeq.pm \
Bio/Seq/RichSeqI.pm \
Bio/Seq/SeqBuilder.pm \
Bio/Seq/SeqFactory.pm \
Bio/Seq/SeqFastaSpeedFactory.pm \
Bio/Seq/SeqWithQuality.pm \
Bio/Seq/SequenceTrace.pm \
Bio/Seq/TraceI.pm \
Bio/SeqAnalysisParserI.pm \
Bio/SeqFeature/AnnotationAdaptor.pm \
Bio/SeqFeature/Collection.pm \
Bio/SeqFeature/CollectionI.pm \
Bio/SeqFeature/Computation.pm \
Bio/SeqFeature/FeaturePair.pm \
Bio/SeqFeature/Gene/Exon.pm \
Bio/SeqFeature/Gene/ExonI.pm \
Bio/SeqFeature/Gene/GeneStructure.pm \
Bio/SeqFeature/Gene/GeneStructureI.pm \
Bio/SeqFeature/Gene/Intron.pm \
Bio/SeqFeature/Gene/NC_Feature.pm \
Bio/SeqFeature/Gene/Poly_A_site.pm \
Bio/SeqFeature/Gene/Promoter.pm \
Bio/SeqFeature/Gene/Transcript.pm \
Bio/SeqFeature/Gene/TranscriptI.pm \
Bio/SeqFeature/Gene/UTR.pm \
Bio/SeqFeature/Generic.pm \
Bio/SeqFeature/PositionProxy.pm \
Bio/SeqFeature/Primer.pm \
Bio/SeqFeature/SiRNA/Oligo.pm \
Bio/SeqFeature/SiRNA/Pair.pm \
Bio/SeqFeature/Similarity.pm \
Bio/SeqFeature/SimilarityPair.pm \
Bio/SeqFeature/Tools/TypeMapper.pm \
Bio/SeqFeature/Tools/Unflattener.pm \
Bio/SeqFeatureI.pm \
Bio/SeqI.pm \
Bio/SeqIO.pm \
Bio/SeqIO/FTHelper.pm \
Bio/SeqIO/MultiFile.pm \
Bio/SeqIO/abi.pm \
Bio/SeqIO/ace.pm \
Bio/SeqIO/alf.pm \
Bio/SeqIO/asciitree.pm \
Bio/SeqIO/bsml.pm \
Bio/SeqIO/chadoxml.pm \
Bio/SeqIO/ctf.pm \
Bio/SeqIO/embl.pm \
Bio/SeqIO/exp.pm \
Bio/SeqIO/fasta.pm \
Bio/SeqIO/fastq.pm \
Bio/SeqIO/game.pm \
Bio/SeqIO/game/featHandler.pm \
Bio/SeqIO/game/gameHandler.pm \
Bio/SeqIO/game/gameSubs.pm \
Bio/SeqIO/game/gameWriter.pm \
Bio/SeqIO/game/seqHandler.pm \
Bio/SeqIO/gcg.pm \
Bio/SeqIO/genbank.pm \
Bio/SeqIO/kegg.pm \
Bio/SeqIO/largefasta.pm \
Bio/SeqIO/locuslink.pm \
Bio/SeqIO/metafasta.pm \
Bio/SeqIO/phd.pm \
Bio/SeqIO/pir.pm \
Bio/SeqIO/pln.pm \
Bio/SeqIO/qual.pm \
Bio/SeqIO/raw.pm \
Bio/SeqIO/scf.pm \
Bio/SeqIO/swiss.pm \
Bio/SeqIO/tab.pm \
Bio/SeqIO/tigr.pm \
Bio/SeqIO/ztr.pm \
Bio/SeqUtils.pm \
Bio/SimpleAlign.pm \
Bio/SimpleAnalysisI.pm \
Bio/Species.pm \
Bio/Structure/Atom.pm \
Bio/Structure/Chain.pm \
Bio/Structure/Entry.pm \
Bio/Structure/IO.pm \
Bio/Structure/IO/pdb.pm \
Bio/Structure/Model.pm \
Bio/Structure/Residue.pm \
Bio/Structure/SecStr/DSSP/Res.pm \
Bio/Structure/SecStr/STRIDE/Res.pm \
Bio/Structure/StructureI.pm \
Bio/Symbol/Alphabet.pm \
Bio/Symbol/AlphabetI.pm \
Bio/Symbol/DNAAlphabet.pm \
Bio/Symbol/ProteinAlphabet.pm \
Bio/Symbol/README.Symbol \
Bio/Symbol/Symbol.pm \
Bio/Symbol/SymbolI.pm \
Bio/Taxonomy.pm \
Bio/Taxonomy/FactoryI.pm \
Bio/Taxonomy/Node.pm \
Bio/Taxonomy/Taxon.pm \
Bio/Taxonomy/Tree.pm \
Bio/Tools/AlignFactory.pm \
Bio/Tools/Alignment/Consed.pm \
Bio/Tools/Alignment/Trim.pm \
Bio/Tools/Analysis/DNA/ESEfinder.pm \
Bio/Tools/Analysis/Protein/Domcut.pm \
Bio/Tools/Analysis/Protein/ELM.pm \
Bio/Tools/Analysis/Protein/GOR4.pm \
Bio/Tools/Analysis/Protein/HNN.pm \
Bio/Tools/Analysis/Protein/Mitoprot.pm \
Bio/Tools/Analysis/Protein/NetPhos.pm \
Bio/Tools/Analysis/Protein/Scansite.pm \
Bio/Tools/Analysis/Protein/Sopma.pm \
Bio/Tools/Analysis/SimpleAnalysisBase.pm \
Bio/Tools/AnalysisResult.pm \
Bio/Tools/BPbl2seq.pm \
Bio/Tools/BPlite.pm \
Bio/Tools/BPlite/HSP.pm \
Bio/Tools/BPlite/Iteration.pm \
Bio/Tools/BPlite/Sbjct.pm \
Bio/Tools/BPpsilite.pm \
Bio/Tools/Blast.pm \
Bio/Tools/Blast/CHANGES \
Bio/Tools/Blast/HSP.pm \
Bio/Tools/Blast/HTML.pm \
Bio/Tools/Blast/README \
Bio/Tools/Blast/Sbjct.pm \
Bio/Tools/Blat.pm \
Bio/Tools/CodonTable.pm \
Bio/Tools/Coil.pm \
Bio/Tools/ECnumber.pm \
Bio/Tools/EMBOSS/Palindrome.pm \
Bio/Tools/EPCR.pm \
Bio/Tools/ESTScan.pm \
Bio/Tools/Eponine.pm \
Bio/Tools/Est2Genome.pm \
Bio/Tools/FootPrinter.pm \
Bio/Tools/GFF.pm \
Bio/Tools/Gel.pm \
Bio/Tools/Geneid.pm \
Bio/Tools/Genemark.pm \
Bio/Tools/Genewise.pm \
Bio/Tools/Genomewise.pm \
Bio/Tools/Genscan.pm \
Bio/Tools/Glimmer.pm \
Bio/Tools/Grail.pm \
Bio/Tools/GuessSeqFormat.pm \
Bio/Tools/HMMER/Domain.pm \
Bio/Tools/HMMER/Results.pm \
Bio/Tools/HMMER/Set.pm \
Bio/Tools/Hmmpfam.pm \
Bio/Tools/IUPAC.pm \
Bio/Tools/Lucy.pm \
Bio/Tools/MZEF.pm \
Bio/Tools/OddCodes.pm \
Bio/Tools/Phylo/Molphy.pm \
Bio/Tools/Phylo/Molphy/Result.pm \
Bio/Tools/Phylo/PAML.pm \
Bio/Tools/Phylo/PAML/ModelResult.pm \
Bio/Tools/Phylo/PAML/Result.pm \
Bio/Tools/Phylo/Phylip/ProtDist.pm \
Bio/Tools/Prediction/Exon.pm \
Bio/Tools/Prediction/Gene.pm \
Bio/Tools/Primer/Assessor/Base.pm \
Bio/Tools/Primer/AssessorI.pm \
Bio/Tools/Primer/Feature.pm \
Bio/Tools/Primer/Pair.pm \
Bio/Tools/Primer3.pm \
Bio/Tools/Prints.pm \
Bio/Tools/Profile.pm \
Bio/Tools/Promoterwise.pm \
Bio/Tools/PrositeScan.pm \
Bio/Tools/Pseudowise.pm \
Bio/Tools/QRNA.pm \
Bio/Tools/RandomDistFunctions.pm \
Bio/Tools/RepeatMasker.pm \
Bio/Tools/RestrictionEnzyme.pm \
Bio/Tools/Run/README \
Bio/Tools/Run/RemoteBlast.pm \
Bio/Tools/Run/StandAloneBlast.pm \
Bio/Tools/Run/WrapperBase.pm \
Bio/Tools/Seg.pm \
Bio/Tools/SeqAnal.pm \
Bio/Tools/SeqPattern.pm \
Bio/Tools/SeqStats.pm \
Bio/Tools/SeqWords.pm \
Bio/Tools/SiRNA.pm \
Bio/Tools/Sigcleave.pm \
Bio/Tools/Signalp.pm \
Bio/Tools/Sim4/Exon.pm \
Bio/Tools/Sim4/Results.pm \
Bio/Tools/Tmhmm.pm \
Bio/Tools/WWW.pm \
Bio/Tools/dpAlign.pm \
Bio/Tools/pICalculator.pm \
Bio/Tools/pSW.pm \
Bio/Tree/AlleleNode.pm \
Bio/Tree/Node.pm \
Bio/Tree/NodeI.pm \
Bio/Tree/NodeNHX.pm \
Bio/Tree/RandomFactory.pm \
Bio/Tree/Statistics.pm \
Bio/Tree/Tree.pm \
Bio/Tree/TreeFunctionsI.pm \
Bio/Tree/TreeI.pm \
Bio/TreeIO.pm \
Bio/TreeIO/TreeEventBuilder.pm \
Bio/TreeIO/lintree.pm \
Bio/TreeIO/newick.pm \
Bio/TreeIO/nexus.pm \
Bio/TreeIO/nhx.pm \
Bio/TreeIO/svggraph.pm \
Bio/TreeIO/tabtree.pm \
Bio/UpdateableSeqI.pm \
Bio/Variation/AAChange.pm \
Bio/Variation/AAReverseMutate.pm \
Bio/Variation/Allele.pm \
Bio/Variation/DNAMutation.pm \
Bio/Variation/IO.pm \
Bio/Variation/IO/flat.pm \
Bio/Variation/IO/xml.pm \
Bio/Variation/README \
Bio/Variation/RNAChange.pm \
Bio/Variation/SNP.pm \
Bio/Variation/SeqDiff.pm \
Bio/Variation/VariantI.pm \
Bio/WebAgent.pm \
biodatabases.pod \
biodesign.pod \
bioperl.pod \
bioscripts.pod \
bptutorial.pl
PM_TO_BLIB = Bio/SeqIO/bsml.pm \
$(INST_LIBDIR)/Bio/SeqIO/bsml.pm \
Bio/Location/NarrowestCoordPolicy.pm \
$(INST_LIBDIR)/Bio/Location/NarrowestCoordPolicy.pm \
Bio/MapIO.pm \
$(INST_LIBDIR)/Bio/MapIO.pm \
Bio/SeqIO/abi.pm \
$(INST_LIBDIR)/Bio/SeqIO/abi.pm \
Bio/OntologyIO/goflat.pm \
$(INST_LIBDIR)/Bio/OntologyIO/goflat.pm \
Bio/Biblio/Organisation.pm \
$(INST_LIBDIR)/Bio/Biblio/Organisation.pm \
Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
Bio/Taxonomy/Taxon.pm \
$(INST_LIBDIR)/Bio/Taxonomy/Taxon.pm \
Bio/DB/GFF/Adaptor/memory.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/memory.pm \
Bio/Graphics/Glyph/redgreen_box.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/redgreen_box.pm \
Bio/Tools/PrositeScan.pm \
$(INST_LIBDIR)/Bio/Tools/PrositeScan.pm \
Bio/Variation/IO.pm \
$(INST_LIBDIR)/Bio/Variation/IO.pm \
Bio/Factory/FTLocationFactory.pm \
$(INST_LIBDIR)/Bio/Factory/FTLocationFactory.pm \
Bio/Tools/ECnumber.pm \
$(INST_LIBDIR)/Bio/Tools/ECnumber.pm \
Bio/SearchIO/Writer/HTMLResultWriter.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/HTMLResultWriter.pm \
Bio/Variation/AAChange.pm \
$(INST_LIBDIR)/Bio/Variation/AAChange.pm \
Bio/Biblio/Book.pm \
$(INST_LIBDIR)/Bio/Biblio/Book.pm \
Bio/DB/GFF/Aggregator/match.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/match.pm \
Bio/Event/EventHandlerI.pm \
$(INST_LIBDIR)/Bio/Event/EventHandlerI.pm \
Bio/DB/GFF/Util/Rearrange.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Util/Rearrange.pm \
Bio/Tools/OddCodes.pm \
$(INST_LIBDIR)/Bio/Tools/OddCodes.pm \
Bio/Factory/ObjectFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/ObjectFactoryI.pm \
Bio/Search/Hit/HitFactory.pm \
$(INST_LIBDIR)/Bio/Search/Hit/HitFactory.pm \
Bio/DB/GFF/Aggregator/clone.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/clone.pm \
Bio/Root/Global.pm \
$(INST_LIBDIR)/Bio/Root/Global.pm \
Bio/Seq.pm \
$(INST_LIBDIR)/Bio/Seq.pm \
Bio/Root/Vector.pm \
$(INST_LIBDIR)/Bio/Root/Vector.pm \
Bio/SearchIO/Writer/TextResultWriter.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/TextResultWriter.pm \
Bio/Tools/HMMER/Set.pm \
$(INST_LIBDIR)/Bio/Tools/HMMER/Set.pm \
Bio/SeqIO/FTHelper.pm \
$(INST_LIBDIR)/Bio/SeqIO/FTHelper.pm \
Bio/LiveSeq/IO/SRS.pm \
$(INST_LIBDIR)/Bio/LiveSeq/IO/SRS.pm \
Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
$(INST_LIBDIR)/Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
Bio/Tools/Analysis/Protein/HNN.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/HNN.pm \
Bio/Tools/BPlite/HSP.pm \
$(INST_LIBDIR)/Bio/Tools/BPlite/HSP.pm \
Bio/Tools/Sigcleave.pm \
$(INST_LIBDIR)/Bio/Tools/Sigcleave.pm \
Bio/SearchIO/Writer/BSMLResultWriter.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/BSMLResultWriter.pm \
Bio/DB/GFF/Adaptor/dbi/pg.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/pg.pm \
Bio/Graphics/Glyph/triangle.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/triangle.pm \
Bio/Assembly/IO/ace.pm \
$(INST_LIBDIR)/Bio/Assembly/IO/ace.pm \
Bio/Map/CytoMap.pm \
$(INST_LIBDIR)/Bio/Map/CytoMap.pm \
Bio/Restriction/IO/bairoch.pm \
$(INST_LIBDIR)/Bio/Restriction/IO/bairoch.pm \
Bio/Graphics/ConfiguratorI.pm \
$(INST_LIBDIR)/Bio/Graphics/ConfiguratorI.pm \
Bio/Structure/IO.pm \
$(INST_LIBDIR)/Bio/Structure/IO.pm \
Bio/Tree/RandomFactory.pm \
$(INST_LIBDIR)/Bio/Tree/RandomFactory.pm \
Bio/Factory/ObjectFactory.pm \
$(INST_LIBDIR)/Bio/Factory/ObjectFactory.pm \
Bio/Matrix/PSM/SiteMatrix.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/SiteMatrix.pm \
Bio/DasI.pm \
$(INST_LIBDIR)/Bio/DasI.pm \
Bio/Matrix/PSM/InstanceSiteI.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/InstanceSiteI.pm \
Bio/Coordinate/ExtrapolatingPair.pm \
$(INST_LIBDIR)/Bio/Coordinate/ExtrapolatingPair.pm \
Bio/SeqIO/pir.pm \
$(INST_LIBDIR)/Bio/SeqIO/pir.pm \
Bio/Tools/SeqAnal.pm \
$(INST_LIBDIR)/Bio/Tools/SeqAnal.pm \
Bio/Annotation/StructuredValue.pm \
$(INST_LIBDIR)/Bio/Annotation/StructuredValue.pm \
Bio/Biblio/Ref.pm \
$(INST_LIBDIR)/Bio/Biblio/Ref.pm \
Bio/SeqIO/phd.pm \
$(INST_LIBDIR)/Bio/SeqIO/phd.pm \
Bio/Tools/Glimmer.pm \
$(INST_LIBDIR)/Bio/Tools/Glimmer.pm \
Bio/CodonUsage/IO.pm \
$(INST_LIBDIR)/Bio/CodonUsage/IO.pm \
Bio/Location/Simple.pm \
$(INST_LIBDIR)/Bio/Location/Simple.pm \
Bio/Map/OrderedPositionWithDistance.pm \
$(INST_LIBDIR)/Bio/Map/OrderedPositionWithDistance.pm \
Bio/Tools/Phylo/PAML/Result.pm \
$(INST_LIBDIR)/Bio/Tools/Phylo/PAML/Result.pm \
Bio/AnnotationCollectionI.pm \
$(INST_LIBDIR)/Bio/AnnotationCollectionI.pm \
Bio/SeqAnalysisParserI.pm \
$(INST_LIBDIR)/Bio/SeqAnalysisParserI.pm \
Bio/Tools/GFF.pm \
$(INST_LIBDIR)/Bio/Tools/GFF.pm \
Bio/Variation/AAReverseMutate.pm \
$(INST_LIBDIR)/Bio/Variation/AAReverseMutate.pm \
Bio/Cluster/ClusterFactory.pm \
$(INST_LIBDIR)/Bio/Cluster/ClusterFactory.pm \
Bio/Tools/SiRNA.pm \
$(INST_LIBDIR)/Bio/Tools/SiRNA.pm \
Bio/SeqIO/qual.pm \
$(INST_LIBDIR)/Bio/SeqIO/qual.pm \
Bio/DB/EMBL.pm \
$(INST_LIBDIR)/Bio/DB/EMBL.pm \
Bio/Tools/SeqWords.pm \
$(INST_LIBDIR)/Bio/Tools/SeqWords.pm \
Bio/DB/UpdateableSeqI.pm \
$(INST_LIBDIR)/Bio/DB/UpdateableSeqI.pm \
Bio/SeqFeature/Computation.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Computation.pm \
Bio/Matrix/IO.pm \
$(INST_LIBDIR)/Bio/Matrix/IO.pm \
Bio/SeqFeature/CollectionI.pm \
$(INST_LIBDIR)/Bio/SeqFeature/CollectionI.pm \
Bio/DB/GFF/Homol.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Homol.pm \
Bio/SeqIO/locuslink.pm \
$(INST_LIBDIR)/Bio/SeqIO/locuslink.pm \
Bio/SeqIO/ctf.pm \
$(INST_LIBDIR)/Bio/SeqIO/ctf.pm \
Bio/SeqUtils.pm \
$(INST_LIBDIR)/Bio/SeqUtils.pm \
Bio/DB/Flat/BDB/embl.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BDB/embl.pm \
Bio/Tools/CodonTable.pm \
$(INST_LIBDIR)/Bio/Tools/CodonTable.pm \
Bio/Variation/README \
$(INST_LIBDIR)/Bio/Variation/README \
Bio/Annotation/Comment.pm \
$(INST_LIBDIR)/Bio/Annotation/Comment.pm \
Bio/Seq/BaseSeqProcessor.pm \
$(INST_LIBDIR)/Bio/Seq/BaseSeqProcessor.pm \
Bio/DB/GFF/Adaptor/dbi.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi.pm \
Bio/Tools/QRNA.pm \
$(INST_LIBDIR)/Bio/Tools/QRNA.pm \
Bio/SeqFeature/Primer.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Primer.pm \
Bio/PopGen/PopStats.pm \
$(INST_LIBDIR)/Bio/PopGen/PopStats.pm \
Bio/DB/SeqI.pm \
$(INST_LIBDIR)/Bio/DB/SeqI.pm \
Bio/Tools/Pseudowise.pm \
$(INST_LIBDIR)/Bio/Tools/Pseudowise.pm \
Bio/Tools/Profile.pm \
$(INST_LIBDIR)/Bio/Tools/Profile.pm \
Bio/ClusterIO/unigene.pm \
$(INST_LIBDIR)/Bio/ClusterIO/unigene.pm \
Bio/LiveSeq/Repeat_Region.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Repeat_Region.pm \
Bio/SeqFeature/Tools/TypeMapper.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Tools/TypeMapper.pm \
Bio/DB/GFF/Aggregator.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator.pm \
Bio/PopGen/PopulationI.pm \
$(INST_LIBDIR)/Bio/PopGen/PopulationI.pm \
Bio/SeqIO/game/seqHandler.pm \
$(INST_LIBDIR)/Bio/SeqIO/game/seqHandler.pm \
Bio/AnalysisResultI.pm \
$(INST_LIBDIR)/Bio/AnalysisResultI.pm \
Bio/Phenotype/MeSH/Term.pm \
$(INST_LIBDIR)/Bio/Phenotype/MeSH/Term.pm \
Bio/Tools/Sim4/Results.pm \
$(INST_LIBDIR)/Bio/Tools/Sim4/Results.pm \
Bio/Seq/PrimedSeq.pm \
$(INST_LIBDIR)/Bio/Seq/PrimedSeq.pm \
Bio/Biblio/MedlineJournalArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/MedlineJournalArticle.pm \
Bio/SeqIO/swiss.pm \
$(INST_LIBDIR)/Bio/SeqIO/swiss.pm \
Bio/SeqFeatureI.pm \
$(INST_LIBDIR)/Bio/SeqFeatureI.pm \
Bio/Biblio/BiblioBase.pm \
$(INST_LIBDIR)/Bio/Biblio/BiblioBase.pm \
Bio/Location/Split.pm \
$(INST_LIBDIR)/Bio/Location/Split.pm \
Bio/DB/GenPept.pm \
$(INST_LIBDIR)/Bio/DB/GenPept.pm \
Bio/DB/GFF/Adaptor/biofetch.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/biofetch.pm \
Bio/Ontology/SimpleGOEngine.pm \
$(INST_LIBDIR)/Bio/Ontology/SimpleGOEngine.pm \
Bio/Graphics/Glyph.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph.pm \
Bio/Graphics/FeatureFile.pm \
$(INST_LIBDIR)/Bio/Graphics/FeatureFile.pm \
Bio/Tree/Node.pm \
$(INST_LIBDIR)/Bio/Tree/Node.pm \
Bio/Symbol/ProteinAlphabet.pm \
$(INST_LIBDIR)/Bio/Symbol/ProteinAlphabet.pm \
Bio/Tools/Prediction/Gene.pm \
$(INST_LIBDIR)/Bio/Tools/Prediction/Gene.pm \
Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
Bio/Seq/MetaI.pm \
$(INST_LIBDIR)/Bio/Seq/MetaI.pm \
Bio/Tools/RepeatMasker.pm \
$(INST_LIBDIR)/Bio/Tools/RepeatMasker.pm \
Bio/LiveSeq/Repeat_Unit.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Repeat_Unit.pm \
Bio/Matrix/PSM/SiteMatrixI.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/SiteMatrixI.pm \
Bio/Tools/BPlite/Sbjct.pm \
$(INST_LIBDIR)/Bio/Tools/BPlite/Sbjct.pm \
Bio/AnnotationI.pm \
$(INST_LIBDIR)/Bio/AnnotationI.pm \
Bio/DB/XEMBL.pm \
$(INST_LIBDIR)/Bio/DB/XEMBL.pm \
Bio/Tools/Geneid.pm \
$(INST_LIBDIR)/Bio/Tools/Geneid.pm \
Bio/Tools/Prints.pm \
$(INST_LIBDIR)/Bio/Tools/Prints.pm \
Bio/Phenotype/Phenotype.pm \
$(INST_LIBDIR)/Bio/Phenotype/Phenotype.pm \
Bio/Tools/GuessSeqFormat.pm \
$(INST_LIBDIR)/Bio/Tools/GuessSeqFormat.pm \
Bio/Coordinate/Chain.pm \
$(INST_LIBDIR)/Bio/Coordinate/Chain.pm \
Bio/SeqIO/chadoxml.pm \
$(INST_LIBDIR)/Bio/SeqIO/chadoxml.pm \
Bio/Matrix/PSM/IO/mast.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/IO/mast.pm \
Bio/Root/IO.pm \
$(INST_LIBDIR)/Bio/Root/IO.pm \
Bio/Graphics/Glyph/transcript2.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/transcript2.pm \
Bio/Index/Swissprot.pm \
$(INST_LIBDIR)/Bio/Index/Swissprot.pm \
Bio/PopGen/GenotypeI.pm \
$(INST_LIBDIR)/Bio/PopGen/GenotypeI.pm \
Bio/Search/HSP/PSLHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/PSLHSP.pm \
Bio/DB/Flat/BDB/genbank.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BDB/genbank.pm \
Bio/DB/GFF/Util/Binning.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Util/Binning.pm \
Bio/Seq/LargePrimarySeq.pm \
$(INST_LIBDIR)/Bio/Seq/LargePrimarySeq.pm \
Bio/DB/GFF.pm \
$(INST_LIBDIR)/Bio/DB/GFF.pm \
Bio/SeqFeature/Gene/NC_Feature.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/NC_Feature.pm \
Bio/SimpleAlign.pm \
$(INST_LIBDIR)/Bio/SimpleAlign.pm \
Bio/SearchDist.pm \
$(INST_LIBDIR)/Bio/SearchDist.pm \
Bio/DB/GFF/Aggregator/alignment.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/alignment.pm \
Bio/Symbol/Alphabet.pm \
$(INST_LIBDIR)/Bio/Symbol/Alphabet.pm \
Bio/Tools/Blast/HTML.pm \
$(INST_LIBDIR)/Bio/Tools/Blast/HTML.pm \
Bio/Tools/Gel.pm \
$(INST_LIBDIR)/Bio/Tools/Gel.pm \
Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
$(INST_LIBDIR)/Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
Bio/Graphics/RendererI.pm \
$(INST_LIBDIR)/Bio/Graphics/RendererI.pm \
Bio/Tools/BPlite.pm \
$(INST_LIBDIR)/Bio/Tools/BPlite.pm \
Bio/AlignIO/selex.pm \
$(INST_LIBDIR)/Bio/AlignIO/selex.pm \
Bio/Factory/TreeFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/TreeFactoryI.pm \
Bio/Range.pm \
$(INST_LIBDIR)/Bio/Range.pm \
Bio/Matrix/Scoring.pm \
$(INST_LIBDIR)/Bio/Matrix/Scoring.pm \
Bio/Annotation/AnnotationFactory.pm \
$(INST_LIBDIR)/Bio/Annotation/AnnotationFactory.pm \
Bio/Tools/Eponine.pm \
$(INST_LIBDIR)/Bio/Tools/Eponine.pm \
Bio/Map/Position.pm \
$(INST_LIBDIR)/Bio/Map/Position.pm \
Bio/Graphics/Util.pm \
$(INST_LIBDIR)/Bio/Graphics/Util.pm \
Bio/Biblio/MedlineBook.pm \
$(INST_LIBDIR)/Bio/Biblio/MedlineBook.pm \
Bio/Graphics/Glyph/diamond.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/diamond.pm \
Bio/Search/Iteration/IterationI.pm \
$(INST_LIBDIR)/Bio/Search/Iteration/IterationI.pm \
Bio/Search/Result/GenericResult.pm \
$(INST_LIBDIR)/Bio/Search/Result/GenericResult.pm \
Bio/Factory/SequenceProcessorI.pm \
$(INST_LIBDIR)/Bio/Factory/SequenceProcessorI.pm \
Bio/Location/SplitLocationI.pm \
$(INST_LIBDIR)/Bio/Location/SplitLocationI.pm \
Bio/SeqIO/exp.pm \
$(INST_LIBDIR)/Bio/SeqIO/exp.pm \
Bio/Assembly/ContigAnalysis.pm \
$(INST_LIBDIR)/Bio/Assembly/ContigAnalysis.pm \
Bio/LiveSeq/DNA.pm \
$(INST_LIBDIR)/Bio/LiveSeq/DNA.pm \
Bio/DB/GFF/Adaptor/ace.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/ace.pm \
Bio/Graphics/Glyph/translation.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/translation.pm \
Bio/Graphics/Glyph/ex.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/ex.pm \
Bio/Seq/LargeSeq.pm \
$(INST_LIBDIR)/Bio/Seq/LargeSeq.pm \
Bio/Tools/Blast/README \
$(INST_LIBDIR)/Bio/Tools/Blast/README \
Bio/SeqIO/metafasta.pm \
$(INST_LIBDIR)/Bio/SeqIO/metafasta.pm \
Bio/Symbol/SymbolI.pm \
$(INST_LIBDIR)/Bio/Symbol/SymbolI.pm \
Bio/Matrix/PSM/Psm.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/Psm.pm \
Bio/Biblio/Thesis.pm \
$(INST_LIBDIR)/Bio/Biblio/Thesis.pm \
Bio/Search/GenericDatabase.pm \
$(INST_LIBDIR)/Bio/Search/GenericDatabase.pm \
Bio/Event/EventGeneratorI.pm \
$(INST_LIBDIR)/Bio/Event/EventGeneratorI.pm \
Bio/Taxonomy/Node.pm \
$(INST_LIBDIR)/Bio/Taxonomy/Node.pm \
Bio/AlignIO/meme.pm \
$(INST_LIBDIR)/Bio/AlignIO/meme.pm \
Bio/DB/GFF/Typename.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Typename.pm \
Bio/Coordinate/Result/Gap.pm \
$(INST_LIBDIR)/Bio/Coordinate/Result/Gap.pm \
Bio/LiveSeq/Intron.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Intron.pm \
Bio/AlignIO/mase.pm \
$(INST_LIBDIR)/Bio/AlignIO/mase.pm \
Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
Bio/SeqIO/pln.pm \
$(INST_LIBDIR)/Bio/SeqIO/pln.pm \
Bio/Structure/Atom.pm \
$(INST_LIBDIR)/Bio/Structure/Atom.pm \
Bio/DB/BioFetch.pm \
$(INST_LIBDIR)/Bio/DB/BioFetch.pm \
Bio/LiveSeq/Gene.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Gene.pm \
Bio/Ontology/TermI.pm \
$(INST_LIBDIR)/Bio/Ontology/TermI.pm \
Bio/DB/GFF/Adaptor/dbi/mysql.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/mysql.pm \
Bio/Biblio/PubmedBookArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/PubmedBookArticle.pm \
Bio/SeqIO/game/featHandler.pm \
$(INST_LIBDIR)/Bio/SeqIO/game/featHandler.pm \
Bio/Tools/Analysis/Protein/NetPhos.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/NetPhos.pm \
Bio/SeqIO/game/gameHandler.pm \
$(INST_LIBDIR)/Bio/SeqIO/game/gameHandler.pm \
Bio/Ontology/InterProTerm.pm \
$(INST_LIBDIR)/Bio/Ontology/InterProTerm.pm \
Bio/Phenotype/PhenotypeI.pm \
$(INST_LIBDIR)/Bio/Phenotype/PhenotypeI.pm \
Bio/Search/Iteration/GenericIteration.pm \
$(INST_LIBDIR)/Bio/Search/Iteration/GenericIteration.pm \
Bio/PopGen/Genotype.pm \
$(INST_LIBDIR)/Bio/PopGen/Genotype.pm \
Bio/Assembly/IO.pm \
$(INST_LIBDIR)/Bio/Assembly/IO.pm \
Bio/DB/GFF/RelSegment.pm \
$(INST_LIBDIR)/Bio/DB/GFF/RelSegment.pm \
Bio/DB/XEMBLService.pm \
$(INST_LIBDIR)/Bio/DB/XEMBLService.pm \
Bio/SearchIO/EventHandlerI.pm \
$(INST_LIBDIR)/Bio/SearchIO/EventHandlerI.pm \
Bio/TreeIO/nhx.pm \
$(INST_LIBDIR)/Bio/TreeIO/nhx.pm \
Bio/Graphics/Glyph/processed_transcript.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/processed_transcript.pm \
Bio/Ontology/TermFactory.pm \
$(INST_LIBDIR)/Bio/Ontology/TermFactory.pm \
Bio/SeqI.pm \
$(INST_LIBDIR)/Bio/SeqI.pm \
Bio/Align/StatisticsI.pm \
$(INST_LIBDIR)/Bio/Align/StatisticsI.pm \
Bio/Matrix/PSM/IO/meme.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/IO/meme.pm \
Bio/Matrix/MatrixI.pm \
$(INST_LIBDIR)/Bio/Matrix/MatrixI.pm \
Bio/Graphics/Glyph/graded_segments.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/graded_segments.pm \
Bio/Matrix/PhylipDist.pm \
$(INST_LIBDIR)/Bio/Matrix/PhylipDist.pm \
Bio/Coordinate/GeneMapper.pm \
$(INST_LIBDIR)/Bio/Coordinate/GeneMapper.pm \
Bio/IdCollectionI.pm \
$(INST_LIBDIR)/Bio/IdCollectionI.pm \
Bio/Cluster/UniGene.pm \
$(INST_LIBDIR)/Bio/Cluster/UniGene.pm \
Bio/Coordinate/ResultI.pm \
$(INST_LIBDIR)/Bio/Coordinate/ResultI.pm \
Bio/Ontology/Ontology.pm \
$(INST_LIBDIR)/Bio/Ontology/Ontology.pm \
Bio/Tools/Blat.pm \
$(INST_LIBDIR)/Bio/Tools/Blat.pm \
Bio/SeqIO/scf.pm \
$(INST_LIBDIR)/Bio/SeqIO/scf.pm \
Bio/LiveSeq/Translation.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Translation.pm \
Bio/LiveSeq/Chain.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Chain.pm \
Bio/Seq/SeqBuilder.pm \
$(INST_LIBDIR)/Bio/Seq/SeqBuilder.pm \
Bio/Align/Utilities.pm \
$(INST_LIBDIR)/Bio/Align/Utilities.pm \
Bio/Root/Version.pm \
$(INST_LIBDIR)/Bio/Root/Version.pm \
Bio/PopGen/Marker.pm \
$(INST_LIBDIR)/Bio/PopGen/Marker.pm \
Bio/Biblio/IO/pubmed2ref.pm \
$(INST_LIBDIR)/Bio/Biblio/IO/pubmed2ref.pm \
Bio/LiveSeq/Mutation.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Mutation.pm \
Bio/Location/AvWithinCoordPolicy.pm \
$(INST_LIBDIR)/Bio/Location/AvWithinCoordPolicy.pm \
Bio/Tools/IUPAC.pm \
$(INST_LIBDIR)/Bio/Tools/IUPAC.pm \
Bio/DB/GFF/Aggregator/processed_transcript.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/processed_transcript.pm \
Bio/Structure/Entry.pm \
$(INST_LIBDIR)/Bio/Structure/Entry.pm \
Bio/Perl.pm \
$(INST_LIBDIR)/Bio/Perl.pm \
Bio/Align/DNAStatistics.pm \
$(INST_LIBDIR)/Bio/Align/DNAStatistics.pm \
Bio/Ontology/OntologyEngineI.pm \
$(INST_LIBDIR)/Bio/Ontology/OntologyEngineI.pm \
Bio/SeqIO/ztr.pm \
$(INST_LIBDIR)/Bio/SeqIO/ztr.pm \
Bio/Tools/SeqPattern.pm \
$(INST_LIBDIR)/Bio/Tools/SeqPattern.pm \
Bio/Factory/LocationFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/LocationFactoryI.pm \
Bio/DB/CUTG.pm \
$(INST_LIBDIR)/Bio/DB/CUTG.pm \
Bio/SearchIO/SearchResultEventBuilder.pm \
$(INST_LIBDIR)/Bio/SearchIO/SearchResultEventBuilder.pm \
Bio/Restriction/EnzymeI.pm \
$(INST_LIBDIR)/Bio/Restriction/EnzymeI.pm \
Bio/SeqFeature/Tools/Unflattener.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Tools/Unflattener.pm \
Bio/ClusterI.pm \
$(INST_LIBDIR)/Bio/ClusterI.pm \
Bio/SeqFeature/Gene/Transcript.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/Transcript.pm \
Bio/Align/PairwiseStatistics.pm \
$(INST_LIBDIR)/Bio/Align/PairwiseStatistics.pm \
Bio/Tools/WWW.pm \
$(INST_LIBDIR)/Bio/Tools/WWW.pm \
Bio/Tools/Tmhmm.pm \
$(INST_LIBDIR)/Bio/Tools/Tmhmm.pm \
Bio/Tools/Alignment/Trim.pm \
$(INST_LIBDIR)/Bio/Tools/Alignment/Trim.pm \
Bio/Tools/ESTScan.pm \
$(INST_LIBDIR)/Bio/Tools/ESTScan.pm \
Bio/SeqIO/asciitree.pm \
$(INST_LIBDIR)/Bio/SeqIO/asciitree.pm \
Bio/Graphics/Glyph/oval.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/oval.pm \
Bio/SearchIO/blasttable.pm \
$(INST_LIBDIR)/Bio/SearchIO/blasttable.pm \
Bio/Tools/Primer/AssessorI.pm \
$(INST_LIBDIR)/Bio/Tools/Primer/AssessorI.pm \
Bio/Variation/IO/xml.pm \
$(INST_LIBDIR)/Bio/Variation/IO/xml.pm \
Bio/Taxonomy/FactoryI.pm \
$(INST_LIBDIR)/Bio/Taxonomy/FactoryI.pm \
Bio/Tools/RandomDistFunctions.pm \
$(INST_LIBDIR)/Bio/Tools/RandomDistFunctions.pm \
Bio/Seq/SeqWithQuality.pm \
$(INST_LIBDIR)/Bio/Seq/SeqWithQuality.pm \
Bio/Graphics/Glyph/ellipse.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/ellipse.pm \
Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
Bio/Biblio/MedlineArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/MedlineArticle.pm \
Bio/LiveSeq/Transcript.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Transcript.pm \
Bio/Tools/MZEF.pm \
$(INST_LIBDIR)/Bio/Tools/MZEF.pm \
Bio/SearchIO/hmmer.pm \
$(INST_LIBDIR)/Bio/SearchIO/hmmer.pm \
Bio/Biblio/Article.pm \
$(INST_LIBDIR)/Bio/Biblio/Article.pm \
Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
Bio/AlignIO/prodom.pm \
$(INST_LIBDIR)/Bio/AlignIO/prodom.pm \
Bio/Graphics/Glyph/Factory.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/Factory.pm \
Bio/Annotation/Collection.pm \
$(INST_LIBDIR)/Bio/Annotation/Collection.pm \
Bio/Restriction/IO/itype2.pm \
$(INST_LIBDIR)/Bio/Restriction/IO/itype2.pm \
biodatabases.pod \
$(INST_LIBDIR)/biodatabases.pod \
Bio/Restriction/EnzymeCollection.pm \
$(INST_LIBDIR)/Bio/Restriction/EnzymeCollection.pm \
Bio/SeqIO/tab.pm \
$(INST_LIBDIR)/Bio/SeqIO/tab.pm \
Bio/SeqFeature/Gene/Promoter.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/Promoter.pm \
Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
Bio/Factory/SeqAnalysisParserFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/SeqAnalysisParserFactoryI.pm \
Bio/Graphics/Feature.pm \
$(INST_LIBDIR)/Bio/Graphics/Feature.pm \
Bio/Restriction/IO/withrefm.pm \
$(INST_LIBDIR)/Bio/Restriction/IO/withrefm.pm \
Bio/DB/Universal.pm \
$(INST_LIBDIR)/Bio/DB/Universal.pm \
Bio/Graphics/Glyph/anchored_arrow.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/anchored_arrow.pm \
Bio/Tools/Grail.pm \
$(INST_LIBDIR)/Bio/Tools/Grail.pm \
Bio/Variation/SNP.pm \
$(INST_LIBDIR)/Bio/Variation/SNP.pm \
Bio/Taxonomy.pm \
$(INST_LIBDIR)/Bio/Taxonomy.pm \
Bio/Variation/DNAMutation.pm \
$(INST_LIBDIR)/Bio/Variation/DNAMutation.pm \
Bio/PrimarySeqI.pm \
$(INST_LIBDIR)/Bio/PrimarySeqI.pm \
Bio/DescribableI.pm \
$(INST_LIBDIR)/Bio/DescribableI.pm \
Bio/Graphics/Glyph/group.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/group.pm \
Bio/Search/Result/ResultI.pm \
$(INST_LIBDIR)/Bio/Search/Result/ResultI.pm \
Bio/Tools/Coil.pm \
$(INST_LIBDIR)/Bio/Tools/Coil.pm \
Bio/Expression/FeatureGroup.pm \
$(INST_LIBDIR)/Bio/Expression/FeatureGroup.pm \
Bio/TreeIO/tabtree.pm \
$(INST_LIBDIR)/Bio/TreeIO/tabtree.pm \
Bio/Coordinate/Graph.pm \
$(INST_LIBDIR)/Bio/Coordinate/Graph.pm \
Bio/DB/Registry.pm \
$(INST_LIBDIR)/Bio/DB/Registry.pm \
Bio/AnnotatableI.pm \
$(INST_LIBDIR)/Bio/AnnotatableI.pm \
biodesign.pod \
$(INST_LIBDIR)/biodesign.pod \
Bio/AlignIO/psi.pm \
$(INST_LIBDIR)/Bio/AlignIO/psi.pm \
Bio/Ontology/Term.pm \
$(INST_LIBDIR)/Bio/Ontology/Term.pm \
Bio/AlignIO/msf.pm \
$(INST_LIBDIR)/Bio/AlignIO/msf.pm \
Bio/Restriction/Enzyme.pm \
$(INST_LIBDIR)/Bio/Restriction/Enzyme.pm \
Bio/Coordinate/Collection.pm \
$(INST_LIBDIR)/Bio/Coordinate/Collection.pm \
Bio/Map/OrderedPosition.pm \
$(INST_LIBDIR)/Bio/Map/OrderedPosition.pm \
Bio/SearchIO/megablast.pm \
$(INST_LIBDIR)/Bio/SearchIO/megablast.pm \
Bio/Search/HSP/GenericHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/GenericHSP.pm \
Bio/Tools/Genewise.pm \
$(INST_LIBDIR)/Bio/Tools/Genewise.pm \
Bio/Graphics/Glyph/toomany.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/toomany.pm \
Bio/TreeIO.pm \
$(INST_LIBDIR)/Bio/TreeIO.pm \
Bio/DB/GFF/Adaptor/memory_iterator.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/memory_iterator.pm \
Bio/Tools/Phylo/PAML.pm \
$(INST_LIBDIR)/Bio/Tools/Phylo/PAML.pm \
Bio/DB/MeSH.pm \
$(INST_LIBDIR)/Bio/DB/MeSH.pm \
Bio/DB/Makefile.PL \
$(INST_LIBDIR)/Bio/DB/Makefile.PL \
Bio/Factory/HitFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/HitFactoryI.pm \
Bio/Map/CytoMarker.pm \
$(INST_LIBDIR)/Bio/Map/CytoMarker.pm \
Bio/Tree/TreeI.pm \
$(INST_LIBDIR)/Bio/Tree/TreeI.pm \
Bio/Assembly/ScaffoldI.pm \
$(INST_LIBDIR)/Bio/Assembly/ScaffoldI.pm \
Bio/Tree/Statistics.pm \
$(INST_LIBDIR)/Bio/Tree/Statistics.pm \
Bio/LiveSeq/Mutator.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Mutator.pm \
Bio/Search/BlastUtils.pm \
$(INST_LIBDIR)/Bio/Search/BlastUtils.pm \
Bio/Tools/BPlite/Iteration.pm \
$(INST_LIBDIR)/Bio/Tools/BPlite/Iteration.pm \
Bio/OntologyIO/InterProParser.pm \
$(INST_LIBDIR)/Bio/OntologyIO/InterProParser.pm \
Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm \
$(INST_LIBDIR)/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm \
Bio/SeqIO.pm \
$(INST_LIBDIR)/Bio/SeqIO.pm \
Bio/Index/Fasta.pm \
$(INST_LIBDIR)/Bio/Index/Fasta.pm \
Bio/DB/GFF/Aggregator/transcript.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/transcript.pm \
bptutorial.pl \
$(INST_LIBDIR)/bptutorial.pl \
Bio/Symbol/AlphabetI.pm \
$(INST_LIBDIR)/Bio/Symbol/AlphabetI.pm \
Bio/SeqIO/game.pm \
$(INST_LIBDIR)/Bio/SeqIO/game.pm \
Bio/Biblio/MedlineBookArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/MedlineBookArticle.pm \
Bio/OntologyIO.pm \
$(INST_LIBDIR)/Bio/OntologyIO.pm \
Bio/SeqIO/tigr.pm \
$(INST_LIBDIR)/Bio/SeqIO/tigr.pm \
Bio/AlignIO/metafasta.pm \
$(INST_LIBDIR)/Bio/AlignIO/metafasta.pm \
Bio/AlignIO/pfam.pm \
$(INST_LIBDIR)/Bio/AlignIO/pfam.pm \
Bio/Map/LinkagePosition.pm \
$(INST_LIBDIR)/Bio/Map/LinkagePosition.pm \
Bio/Ontology/PathI.pm \
$(INST_LIBDIR)/Bio/Ontology/PathI.pm \
Bio/SeqIO/raw.pm \
$(INST_LIBDIR)/Bio/SeqIO/raw.pm \
Bio/Tools/BPbl2seq.pm \
$(INST_LIBDIR)/Bio/Tools/BPbl2seq.pm \
Bio/Search/HSP/PsiBlastHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/PsiBlastHSP.pm \
Bio/SeqFeature/Gene/GeneStructureI.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/GeneStructureI.pm \
Bio/AlignIO/bl2seq.pm \
$(INST_LIBDIR)/Bio/AlignIO/bl2seq.pm \
Bio/Tools/Primer/Feature.pm \
$(INST_LIBDIR)/Bio/Tools/Primer/Feature.pm \
Bio/Tools/Phylo/Molphy/Result.pm \
$(INST_LIBDIR)/Bio/Tools/Phylo/Molphy/Result.pm \
Bio/Tools/Analysis/SimpleAnalysisBase.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/SimpleAnalysisBase.pm \
Bio/SeqFeature/Gene/UTR.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/UTR.pm \
Bio/DBLinkContainerI.pm \
$(INST_LIBDIR)/Bio/DBLinkContainerI.pm \
Bio/SearchIO/Writer/HSPTableWriter.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/HSPTableWriter.pm \
Bio/SearchIO/axt.pm \
$(INST_LIBDIR)/Bio/SearchIO/axt.pm \
Bio/SeqIO/kegg.pm \
$(INST_LIBDIR)/Bio/SeqIO/kegg.pm \
Bio/Tools/Genomewise.pm \
$(INST_LIBDIR)/Bio/Tools/Genomewise.pm \
Bio/DB/Ace.pm \
$(INST_LIBDIR)/Bio/DB/Ace.pm \
Bio/SearchIO/psl.pm \
$(INST_LIBDIR)/Bio/SearchIO/psl.pm \
Bio/Map/CytoPosition.pm \
$(INST_LIBDIR)/Bio/Map/CytoPosition.pm \
Bio/Index/SwissPfam.pm \
$(INST_LIBDIR)/Bio/Index/SwissPfam.pm \
Bio/Restriction/IO/base.pm \
$(INST_LIBDIR)/Bio/Restriction/IO/base.pm \
Bio/DB/Taxonomy.pm \
$(INST_LIBDIR)/Bio/DB/Taxonomy.pm \
Bio/Graphics/Glyph/splice_site.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/splice_site.pm \
Bio/Factory/ObjectBuilderI.pm \
$(INST_LIBDIR)/Bio/Factory/ObjectBuilderI.pm \
Bio/Tools/Est2Genome.pm \
$(INST_LIBDIR)/Bio/Tools/Est2Genome.pm \
Bio/AlignIO/emboss.pm \
$(INST_LIBDIR)/Bio/AlignIO/emboss.pm \
Bio/Index/Fastq.pm \
$(INST_LIBDIR)/Bio/Index/Fastq.pm \
Bio/DB/Flat/BDB/fasta.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BDB/fasta.pm \
Bio/Tools/Run/WrapperBase.pm \
$(INST_LIBDIR)/Bio/Tools/Run/WrapperBase.pm \
Bio/Annotation/Reference.pm \
$(INST_LIBDIR)/Bio/Annotation/Reference.pm \
Bio/Biblio/PubmedArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/PubmedArticle.pm \
Bio/Root/Err.pm \
$(INST_LIBDIR)/Bio/Root/Err.pm \
Bio/Matrix/PSM/PsmHeader.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/PsmHeader.pm \
Bio/Graphics/Glyph/rndrect.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/rndrect.pm \
Bio/Ontology/SimpleOntologyEngine.pm \
$(INST_LIBDIR)/Bio/Ontology/SimpleOntologyEngine.pm \
Bio/AnalysisI.pm \
$(INST_LIBDIR)/Bio/AnalysisI.pm \
Bio/Annotation/DBLink.pm \
$(INST_LIBDIR)/Bio/Annotation/DBLink.pm \
Bio/Seq/TraceI.pm \
$(INST_LIBDIR)/Bio/Seq/TraceI.pm \
Bio/PopGen/Individual.pm \
$(INST_LIBDIR)/Bio/PopGen/Individual.pm \
Bio/DB/Flat/BDB.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BDB.pm \
Bio/DB/DBFetch.pm \
$(INST_LIBDIR)/Bio/DB/DBFetch.pm \
Bio/Seq/SequenceTrace.pm \
$(INST_LIBDIR)/Bio/Seq/SequenceTrace.pm \
Bio/Graphics/Glyph/box.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/box.pm \
Bio/SearchIO/SearchWriterI.pm \
$(INST_LIBDIR)/Bio/SearchIO/SearchWriterI.pm \
Bio/Graphics/Glyph/redgreen_segment.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/redgreen_segment.pm \
Bio/Graphics/Glyph/span.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/span.pm \
Bio/SearchIO/blast.pm \
$(INST_LIBDIR)/Bio/SearchIO/blast.pm \
Bio/Biblio/IO/medlinexml.pm \
$(INST_LIBDIR)/Bio/Biblio/IO/medlinexml.pm \
Bio/DB/Flat/BDB/swissprot.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BDB/swissprot.pm \
Bio/Tools/Alignment/Consed.pm \
$(INST_LIBDIR)/Bio/Tools/Alignment/Consed.pm \
Bio/SeqFeature/Generic.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Generic.pm \
Bio/SeqFeature/Gene/GeneStructure.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/GeneStructure.pm \
Bio/Ontology/Path.pm \
$(INST_LIBDIR)/Bio/Ontology/Path.pm \
Bio/Tools/Run/RemoteBlast.pm \
$(INST_LIBDIR)/Bio/Tools/Run/RemoteBlast.pm \
Bio/Tools/EMBOSS/Palindrome.pm \
$(INST_LIBDIR)/Bio/Tools/EMBOSS/Palindrome.pm \
Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
Bio/Search/SearchUtils.pm \
$(INST_LIBDIR)/Bio/Search/SearchUtils.pm \
Bio/Root/HTTPget.pm \
$(INST_LIBDIR)/Bio/Root/HTTPget.pm \
Bio/Structure/SecStr/STRIDE/Res.pm \
$(INST_LIBDIR)/Bio/Structure/SecStr/STRIDE/Res.pm \
Bio/Map/MappableI.pm \
$(INST_LIBDIR)/Bio/Map/MappableI.pm \
Bio/Root/Xref.pm \
$(INST_LIBDIR)/Bio/Root/Xref.pm \
Bio/Search/Hit/HMMERHit.pm \
$(INST_LIBDIR)/Bio/Search/Hit/HMMERHit.pm \
Bio/Graphics/Glyph/minmax.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/minmax.pm \
Bio/Symbol/README.Symbol \
$(INST_LIBDIR)/Bio/Symbol/README.Symbol \
Bio/Graphics/Glyph/cds.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/cds.pm \
Bio/SearchIO/Writer/GbrowseGFF.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/GbrowseGFF.pm \
Bio/Biblio/IO/pubmedxml.pm \
$(INST_LIBDIR)/Bio/Biblio/IO/pubmedxml.pm \
Bio/Coordinate/Result/Match.pm \
$(INST_LIBDIR)/Bio/Coordinate/Result/Match.pm \
Bio/Graphics/Glyph/track.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/track.pm \
Bio/Root/Object.pm \
$(INST_LIBDIR)/Bio/Root/Object.pm \
Bio/DB/GFF/Adaptor/dbi/oracle.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/oracle.pm \
Bio/Search/DatabaseI.pm \
$(INST_LIBDIR)/Bio/Search/DatabaseI.pm \
Bio/SeqIO/ace.pm \
$(INST_LIBDIR)/Bio/SeqIO/ace.pm \
Bio/Location/FuzzyLocationI.pm \
$(INST_LIBDIR)/Bio/Location/FuzzyLocationI.pm \
Bio/OntologyIO/Handlers/InterProHandler.pm \
$(INST_LIBDIR)/Bio/OntologyIO/Handlers/InterProHandler.pm \
Bio/Search/Result/ResultFactory.pm \
$(INST_LIBDIR)/Bio/Search/Result/ResultFactory.pm \
Bio/Factory/ResultFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/ResultFactoryI.pm \
Bio/FeatureHolderI.pm \
$(INST_LIBDIR)/Bio/FeatureHolderI.pm \
Bio/DB/QueryI.pm \
$(INST_LIBDIR)/Bio/DB/QueryI.pm \
Bio/Tools/AnalysisResult.pm \
$(INST_LIBDIR)/Bio/Tools/AnalysisResult.pm \
Bio/Biblio/BookArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/BookArticle.pm \
Bio/DB/MANIFEST \
$(INST_LIBDIR)/Bio/DB/MANIFEST \
Bio/Matrix/PSM/PsmHeaderI.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/PsmHeaderI.pm \
Bio/Seq/RichSeqI.pm \
$(INST_LIBDIR)/Bio/Seq/RichSeqI.pm \
Bio/ClusterIO/dbsnp.pm \
$(INST_LIBDIR)/Bio/ClusterIO/dbsnp.pm \
Bio/LiveSeq/IO/Loader.pm \
$(INST_LIBDIR)/Bio/LiveSeq/IO/Loader.pm \
Bio/Variation/IO/flat.pm \
$(INST_LIBDIR)/Bio/Variation/IO/flat.pm \
Bio/CodonUsage/Table.pm \
$(INST_LIBDIR)/Bio/CodonUsage/Table.pm \
Bio/Structure/Chain.pm \
$(INST_LIBDIR)/Bio/Structure/Chain.pm \
Bio/LiveSeq/AARange.pm \
$(INST_LIBDIR)/Bio/LiveSeq/AARange.pm \
Bio/AlignIO/mega.pm \
$(INST_LIBDIR)/Bio/AlignIO/mega.pm \
Bio/DB/FileCache.pm \
$(INST_LIBDIR)/Bio/DB/FileCache.pm \
Bio/Assembly/Contig.pm \
$(INST_LIBDIR)/Bio/Assembly/Contig.pm \
Bio/Root/RootI.pm \
$(INST_LIBDIR)/Bio/Root/RootI.pm \
Bio/AnalysisParserI.pm \
$(INST_LIBDIR)/Bio/AnalysisParserI.pm \
Bio/DB/Taxonomy/flatfile.pm \
$(INST_LIBDIR)/Bio/DB/Taxonomy/flatfile.pm \
Bio/Search/HSP/HMMERHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/HMMERHSP.pm \
Bio/Tools/BPpsilite.pm \
$(INST_LIBDIR)/Bio/Tools/BPpsilite.pm \
Bio/Ontology/Relationship.pm \
$(INST_LIBDIR)/Bio/Ontology/Relationship.pm \
Bio/DB/GenBank.pm \
$(INST_LIBDIR)/Bio/DB/GenBank.pm \
Bio/Tools/Hmmpfam.pm \
$(INST_LIBDIR)/Bio/Tools/Hmmpfam.pm \
Bio/Tools/Phylo/Molphy.pm \
$(INST_LIBDIR)/Bio/Tools/Phylo/Molphy.pm \
Bio/Variation/VariantI.pm \
$(INST_LIBDIR)/Bio/Variation/VariantI.pm \
Bio/LocatableSeq.pm \
$(INST_LIBDIR)/Bio/LocatableSeq.pm \
Bio/Tools/Sim4/Exon.pm \
$(INST_LIBDIR)/Bio/Tools/Sim4/Exon.pm \
Bio/OntologyIO/dagflat.pm \
$(INST_LIBDIR)/Bio/OntologyIO/dagflat.pm \
Bio/Graphics/Glyph/heterogeneous_segments.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/heterogeneous_segments.pm \
Bio/AlignIO/nexus.pm \
$(INST_LIBDIR)/Bio/AlignIO/nexus.pm \
Bio/Biblio/Patent.pm \
$(INST_LIBDIR)/Bio/Biblio/Patent.pm \
Bio/Tools/Phylo/Phylip/ProtDist.pm \
$(INST_LIBDIR)/Bio/Tools/Phylo/Phylip/ProtDist.pm \
Bio/SeqIO/alf.pm \
$(INST_LIBDIR)/Bio/SeqIO/alf.pm \
Bio/Location/WidestCoordPolicy.pm \
$(INST_LIBDIR)/Bio/Location/WidestCoordPolicy.pm \
Bio/DB/Query/GenBank.pm \
$(INST_LIBDIR)/Bio/DB/Query/GenBank.pm \
Bio/Annotation/SimpleValue.pm \
$(INST_LIBDIR)/Bio/Annotation/SimpleValue.pm \
Bio/Biblio/MedlineJournal.pm \
$(INST_LIBDIR)/Bio/Biblio/MedlineJournal.pm \
Bio/Root/IOManager.pm \
$(INST_LIBDIR)/Bio/Root/IOManager.pm \
Bio/OntologyIO/soflat.pm \
$(INST_LIBDIR)/Bio/OntologyIO/soflat.pm \
Bio/Restriction/Enzyme/MultiCut.pm \
$(INST_LIBDIR)/Bio/Restriction/Enzyme/MultiCut.pm \
Bio/DB/Biblio/biofetch.pm \
$(INST_LIBDIR)/Bio/DB/Biblio/biofetch.pm \
Bio/Biblio/Proceeding.pm \
$(INST_LIBDIR)/Bio/Biblio/Proceeding.pm \
Bio/Graphics/Glyph/alignment.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/alignment.pm \
Bio/Biblio/Journal.pm \
$(INST_LIBDIR)/Bio/Biblio/Journal.pm \
Bio/Graphics/Glyph/segmented_keyglyph.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/segmented_keyglyph.pm \
Bio/Graphics/Glyph/transcript.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/transcript.pm \
Bio/Cluster/SequenceFamily.pm \
$(INST_LIBDIR)/Bio/Cluster/SequenceFamily.pm \
Bio/Tree/TreeFunctionsI.pm \
$(INST_LIBDIR)/Bio/Tree/TreeFunctionsI.pm \
Bio/LocationI.pm \
$(INST_LIBDIR)/Bio/LocationI.pm \
Bio/Biblio/Provider.pm \
$(INST_LIBDIR)/Bio/Biblio/Provider.pm \
Bio/Biblio/Person.pm \
$(INST_LIBDIR)/Bio/Biblio/Person.pm \
Bio/AlignIO/phylip.pm \
$(INST_LIBDIR)/Bio/AlignIO/phylip.pm \
Bio/DB/WebDBSeqI.pm \
$(INST_LIBDIR)/Bio/DB/WebDBSeqI.pm \
Bio/DB/Flat/BinarySearch.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BinarySearch.pm \
Bio/Graphics.pm \
$(INST_LIBDIR)/Bio/Graphics.pm \
Bio/Search/Hit/Fasta.pm \
$(INST_LIBDIR)/Bio/Search/Hit/Fasta.pm \
Bio/Graphics/Glyph/ruler_arrow.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/ruler_arrow.pm \
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
Bio/Ontology/RelationshipI.pm \
$(INST_LIBDIR)/Bio/Ontology/RelationshipI.pm \
Bio/Search/HSP/HSPFactory.pm \
$(INST_LIBDIR)/Bio/Search/HSP/HSPFactory.pm \
Bio/Root/Exception.pm \
$(INST_LIBDIR)/Bio/Root/Exception.pm \
Bio/Ontology/OntologyStore.pm \
$(INST_LIBDIR)/Bio/Ontology/OntologyStore.pm \
Bio/Search/Processor.pm \
$(INST_LIBDIR)/Bio/Search/Processor.pm \
Bio/Variation/Allele.pm \
$(INST_LIBDIR)/Bio/Variation/Allele.pm \
Bio/SeqFeature/FeaturePair.pm \
$(INST_LIBDIR)/Bio/SeqFeature/FeaturePair.pm \
Bio/Annotation/OntologyTerm.pm \
$(INST_LIBDIR)/Bio/Annotation/OntologyTerm.pm \
Bio/Biblio/PubmedJournalArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/PubmedJournalArticle.pm \
Bio/TreeIO/TreeEventBuilder.pm \
$(INST_LIBDIR)/Bio/TreeIO/TreeEventBuilder.pm \
Bio/SeqIO/embl.pm \
$(INST_LIBDIR)/Bio/SeqIO/embl.pm \
Bio/WebAgent.pm \
$(INST_LIBDIR)/Bio/WebAgent.pm \
Bio/Biblio/IO/medline2ref.pm \
$(INST_LIBDIR)/Bio/Biblio/IO/medline2ref.pm \
Bio/SearchIO/FastHitEventBuilder.pm \
$(INST_LIBDIR)/Bio/SearchIO/FastHitEventBuilder.pm \
Bio/Tree/NodeI.pm \
$(INST_LIBDIR)/Bio/Tree/NodeI.pm \
Bio/Search/Hit/HitI.pm \
$(INST_LIBDIR)/Bio/Search/Hit/HitI.pm \
Bio/Phenotype/MeSH/Twig.pm \
$(INST_LIBDIR)/Bio/Phenotype/MeSH/Twig.pm \
Bio/Seq/PrimaryQual.pm \
$(INST_LIBDIR)/Bio/Seq/PrimaryQual.pm \
Bio/DB/NCBIHelper.pm \
$(INST_LIBDIR)/Bio/DB/NCBIHelper.pm \
Bio/Graphics/Glyph/xyplot.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/xyplot.pm \
Bio/Annotation/TypeManager.pm \
$(INST_LIBDIR)/Bio/Annotation/TypeManager.pm \
Bio/Tools/Analysis/Protein/Sopma.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Sopma.pm \
Bio/Structure/StructureI.pm \
$(INST_LIBDIR)/Bio/Structure/StructureI.pm \
Bio/SeqIO/largefasta.pm \
$(INST_LIBDIR)/Bio/SeqIO/largefasta.pm \
Bio/Matrix/PSM/InstanceSite.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/InstanceSite.pm \
Bio/Tools/dpAlign.pm \
$(INST_LIBDIR)/Bio/Tools/dpAlign.pm \
Bio/Align/AlignI.pm \
$(INST_LIBDIR)/Bio/Align/AlignI.pm \
Bio/SeqFeature/PositionProxy.pm \
$(INST_LIBDIR)/Bio/SeqFeature/PositionProxy.pm \
Bio/Index/Abstract.pm \
$(INST_LIBDIR)/Bio/Index/Abstract.pm \
Bio/AlignIO.pm \
$(INST_LIBDIR)/Bio/AlignIO.pm \
Bio/Factory/SeqAnalysisParserFactory.pm \
$(INST_LIBDIR)/Bio/Factory/SeqAnalysisParserFactory.pm \
Bio/Biblio.pm \
$(INST_LIBDIR)/Bio/Biblio.pm \
Bio/Restriction/Analysis.pm \
$(INST_LIBDIR)/Bio/Restriction/Analysis.pm \
Bio/Matrix/PSM/IO.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/IO.pm \
Bio/Seq/SeqFastaSpeedFactory.pm \
$(INST_LIBDIR)/Bio/Seq/SeqFastaSpeedFactory.pm \
Bio/Factory/SequenceFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/SequenceFactoryI.pm \
Bio/Structure/Residue.pm \
$(INST_LIBDIR)/Bio/Structure/Residue.pm \
Bio/SeqIO/fasta.pm \
$(INST_LIBDIR)/Bio/SeqIO/fasta.pm \
Bio/PopGen/IO/prettybase.pm \
$(INST_LIBDIR)/Bio/PopGen/IO/prettybase.pm \
Bio/AlignIO/maf.pm \
$(INST_LIBDIR)/Bio/AlignIO/maf.pm \
Bio/Restriction/Enzyme/MultiSite.pm \
$(INST_LIBDIR)/Bio/Restriction/Enzyme/MultiSite.pm \
Bio/Search/Result/HMMERResult.pm \
$(INST_LIBDIR)/Bio/Search/Result/HMMERResult.pm \
Bio/Tools/FootPrinter.pm \
$(INST_LIBDIR)/Bio/Tools/FootPrinter.pm \
Bio/Tools/Analysis/Protein/GOR4.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/GOR4.pm \
Bio/Search/Result/BlastResult.pm \
$(INST_LIBDIR)/Bio/Search/Result/BlastResult.pm \
Bio/MapIO/mapmaker.pm \
$(INST_LIBDIR)/Bio/MapIO/mapmaker.pm \
Bio/Tools/Blast.pm \
$(INST_LIBDIR)/Bio/Tools/Blast.pm \
Bio/Graphics/Glyph/dot.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/dot.pm \
Bio/Seq/Meta/Array.pm \
$(INST_LIBDIR)/Bio/Seq/Meta/Array.pm \
bioperl.pod \
$(INST_LIBDIR)/bioperl.pod \
Bio/Structure/IO/pdb.pm \
$(INST_LIBDIR)/Bio/Structure/IO/pdb.pm \
Bio/Map/LinkageMap.pm \
$(INST_LIBDIR)/Bio/Map/LinkageMap.pm \
Bio/DB/SwissProt.pm \
$(INST_LIBDIR)/Bio/DB/SwissProt.pm \
Bio/Matrix/PSM/IO/transfac.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/IO/transfac.pm \
Bio/Tools/Signalp.pm \
$(INST_LIBDIR)/Bio/Tools/Signalp.pm \
Bio/Phenotype/Measure.pm \
$(INST_LIBDIR)/Bio/Phenotype/Measure.pm \
Bio/Factory/ApplicationFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/ApplicationFactoryI.pm \
Bio/SeqFeature/Gene/TranscriptI.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/TranscriptI.pm \
Bio/LiveSeq/Range.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Range.pm \
Bio/Coordinate/Utils.pm \
$(INST_LIBDIR)/Bio/Coordinate/Utils.pm \
Bio/Search/Result/WABAResult.pm \
$(INST_LIBDIR)/Bio/Search/Result/WABAResult.pm \
Bio/DB/RandomAccessI.pm \
$(INST_LIBDIR)/Bio/DB/RandomAccessI.pm \
Bio/PopGen/Simulation/GeneticDrift.pm \
$(INST_LIBDIR)/Bio/PopGen/Simulation/GeneticDrift.pm \
Bio/DB/GFF/Feature.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Feature.pm \
Bio/Tools/Blast/CHANGES \
$(INST_LIBDIR)/Bio/Tools/Blast/CHANGES \
Bio/DB/Biblio/soap.pm \
$(INST_LIBDIR)/Bio/DB/Biblio/soap.pm \
Bio/DB/Failover.pm \
$(INST_LIBDIR)/Bio/DB/Failover.pm \
Bio/Tools/HMMER/Results.pm \
$(INST_LIBDIR)/Bio/Tools/HMMER/Results.pm \
Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
Bio/Variation/RNAChange.pm \
$(INST_LIBDIR)/Bio/Variation/RNAChange.pm \
Bio/Tools/Run/README \
$(INST_LIBDIR)/Bio/Tools/Run/README \
Bio/TreeIO/lintree.pm \
$(INST_LIBDIR)/Bio/TreeIO/lintree.pm \
Bio/Graphics/Pictogram.pm \
$(INST_LIBDIR)/Bio/Graphics/Pictogram.pm \
Bio/Factory/AnalysisI.pm \
$(INST_LIBDIR)/Bio/Factory/AnalysisI.pm \
Bio/Expression/FeatureGroup/FeatureGroupMas50.pm \
$(INST_LIBDIR)/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm \
Bio/Graphics/Glyph/dna.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/dna.pm \
Bio/Phenotype/OMIM/OMIMparser.pm \
$(INST_LIBDIR)/Bio/Phenotype/OMIM/OMIMparser.pm \
Bio/SeqFeature/SiRNA/Pair.pm \
$(INST_LIBDIR)/Bio/SeqFeature/SiRNA/Pair.pm \
Bio/SeqFeature/Similarity.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Similarity.pm \
Bio/Location/CoordinatePolicyI.pm \
$(INST_LIBDIR)/Bio/Location/CoordinatePolicyI.pm \
Bio/Expression/FeatureI.pm \
$(INST_LIBDIR)/Bio/Expression/FeatureI.pm \
Bio/SeqIO/fastq.pm \
$(INST_LIBDIR)/Bio/SeqIO/fastq.pm \
Bio/Tools/Genscan.pm \
$(INST_LIBDIR)/Bio/Tools/Genscan.pm \
Bio/Graphics/Glyph/generic.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/generic.pm \
Bio/Map/SimpleMap.pm \
$(INST_LIBDIR)/Bio/Map/SimpleMap.pm \
Bio/Search/Hit/PsiBlastHit.pm \
$(INST_LIBDIR)/Bio/Search/Hit/PsiBlastHit.pm \
Bio/Search/HSP/WABAHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/WABAHSP.pm \
Bio/SearchIO/Writer/ResultTableWriter.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/ResultTableWriter.pm \
Bio/AlignIO/fasta.pm \
$(INST_LIBDIR)/Bio/AlignIO/fasta.pm \
Bio/Map/Marker.pm \
$(INST_LIBDIR)/Bio/Map/Marker.pm \
Bio/Factory/SequenceStreamI.pm \
$(INST_LIBDIR)/Bio/Factory/SequenceStreamI.pm \
Bio/AlignIO/clustalw.pm \
$(INST_LIBDIR)/Bio/AlignIO/clustalw.pm \
Bio/Coordinate/MapperI.pm \
$(INST_LIBDIR)/Bio/Coordinate/MapperI.pm \
Bio/DB/Fasta.pm \
$(INST_LIBDIR)/Bio/DB/Fasta.pm \
Bio/DB/GFF/Adaptor/dbi/iterator.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/iterator.pm \
Bio/Phenotype/OMIM/OMIMentry.pm \
$(INST_LIBDIR)/Bio/Phenotype/OMIM/OMIMentry.pm \
Bio/Seq/QualI.pm \
$(INST_LIBDIR)/Bio/Seq/QualI.pm \
Bio/Tools/Analysis/Protein/Scansite.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Scansite.pm \
Bio/Tools/HMMER/Domain.pm \
$(INST_LIBDIR)/Bio/Tools/HMMER/Domain.pm \
Bio/Graphics/FeatureFile/Iterator.pm \
$(INST_LIBDIR)/Bio/Graphics/FeatureFile/Iterator.pm \
Bio/Das/FeatureTypeI.pm \
$(INST_LIBDIR)/Bio/Das/FeatureTypeI.pm \
Bio/DB/GDB.pm \
$(INST_LIBDIR)/Bio/DB/GDB.pm \
Bio/Cluster/UniGeneI.pm \
$(INST_LIBDIR)/Bio/Cluster/UniGeneI.pm \
Bio/Biblio/JournalArticle.pm \
$(INST_LIBDIR)/Bio/Biblio/JournalArticle.pm \
Bio/Tools/Blast/Sbjct.pm \
$(INST_LIBDIR)/Bio/Tools/Blast/Sbjct.pm \
Bio/Index/EMBL.pm \
$(INST_LIBDIR)/Bio/Index/EMBL.pm \
Bio/Das/SegmentI.pm \
$(INST_LIBDIR)/Bio/Das/SegmentI.pm \
Bio/Search/Hit/GenericHit.pm \
$(INST_LIBDIR)/Bio/Search/Hit/GenericHit.pm \
Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
Bio/Ontology/OntologyI.pm \
$(INST_LIBDIR)/Bio/Ontology/OntologyI.pm \
Bio/DB/GFF/Segment.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Segment.pm \
Bio/SeqIO/gcg.pm \
$(INST_LIBDIR)/Bio/SeqIO/gcg.pm \
Bio/Tools/Lucy.pm \
$(INST_LIBDIR)/Bio/Tools/Lucy.pm \
Bio/Biblio/WebResource.pm \
$(INST_LIBDIR)/Bio/Biblio/WebResource.pm \
Bio/TreeIO/svggraph.pm \
$(INST_LIBDIR)/Bio/TreeIO/svggraph.pm \
Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
Bio/SeqFeature/Gene/Poly_A_site.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/Poly_A_site.pm \
Bio/RangeI.pm \
$(INST_LIBDIR)/Bio/RangeI.pm \
Bio/Symbol/DNAAlphabet.pm \
$(INST_LIBDIR)/Bio/Symbol/DNAAlphabet.pm \
Bio/Tools/Analysis/Protein/ELM.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/ELM.pm \
Bio/PrimarySeq.pm \
$(INST_LIBDIR)/Bio/PrimarySeq.pm \
Bio/Biblio/TechReport.pm \
$(INST_LIBDIR)/Bio/Biblio/TechReport.pm \
Bio/Seq/EncodedSeq.pm \
$(INST_LIBDIR)/Bio/Seq/EncodedSeq.pm \
Bio/PopGen/IndividualI.pm \
$(INST_LIBDIR)/Bio/PopGen/IndividualI.pm \
Bio/Factory/MapFactoryI.pm \
$(INST_LIBDIR)/Bio/Factory/MapFactoryI.pm \
Bio/Ontology/RelationshipFactory.pm \
$(INST_LIBDIR)/Bio/Ontology/RelationshipFactory.pm \
Bio/Tree/NodeNHX.pm \
$(INST_LIBDIR)/Bio/Tree/NodeNHX.pm \
Bio/SearchIO.pm \
$(INST_LIBDIR)/Bio/SearchIO.pm \
Bio/LiveSeq/SeqI.pm \
$(INST_LIBDIR)/Bio/LiveSeq/SeqI.pm \
Bio/Tools/Genemark.pm \
$(INST_LIBDIR)/Bio/Tools/Genemark.pm \
Bio/Graphics/Glyph/extending_arrow.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/extending_arrow.pm \
Bio/DB/GFF/Aggregator/coding.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/coding.pm \
Bio/SearchIO/exonerate.pm \
$(INST_LIBDIR)/Bio/SearchIO/exonerate.pm \
Bio/Graphics/Glyph/segments.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/segments.pm \
Bio/DB/GFF/Aggregator/none.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/none.pm \
Bio/SeqFeature/SimilarityPair.pm \
$(INST_LIBDIR)/Bio/SeqFeature/SimilarityPair.pm \
Bio/Ontology/RelationshipType.pm \
$(INST_LIBDIR)/Bio/Ontology/RelationshipType.pm \
Bio/Structure/SecStr/DSSP/Res.pm \
$(INST_LIBDIR)/Bio/Structure/SecStr/DSSP/Res.pm \
Bio/PopGen/Population.pm \
$(INST_LIBDIR)/Bio/PopGen/Population.pm \
Bio/PopGen/Simulation/Coalescent.pm \
$(INST_LIBDIR)/Bio/PopGen/Simulation/Coalescent.pm \
Bio/PopGen/Statistics.pm \
$(INST_LIBDIR)/Bio/PopGen/Statistics.pm \
Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
Bio/Structure/Model.pm \
$(INST_LIBDIR)/Bio/Structure/Model.pm \
Bio/Search/HSP/HSPI.pm \
$(INST_LIBDIR)/Bio/Search/HSP/HSPI.pm \
Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
Bio/Index/AbstractSeq.pm \
$(INST_LIBDIR)/Bio/Index/AbstractSeq.pm \
Bio/Seq/RichSeq.pm \
$(INST_LIBDIR)/Bio/Seq/RichSeq.pm \
Bio/Expression/FeatureSet/FeatureSetMas50.pm \
$(INST_LIBDIR)/Bio/Expression/FeatureSet/FeatureSetMas50.pm \
Bio/Tree/AlleleNode.pm \
$(INST_LIBDIR)/Bio/Tree/AlleleNode.pm \
Bio/DB/RefSeq.pm \
$(INST_LIBDIR)/Bio/DB/RefSeq.pm \
bioscripts.pod \
$(INST_LIBDIR)/bioscripts.pod \
Bio/DB/InMemoryCache.pm \
$(INST_LIBDIR)/Bio/DB/InMemoryCache.pm \
Bio/ClusterIO.pm \
$(INST_LIBDIR)/Bio/ClusterIO.pm \
Bio/TreeIO/nexus.pm \
$(INST_LIBDIR)/Bio/TreeIO/nexus.pm \
Bio/Graphics/Panel.pm \
$(INST_LIBDIR)/Bio/Graphics/Panel.pm \
Bio/Cluster/FamilyI.pm \
$(INST_LIBDIR)/Bio/Cluster/FamilyI.pm \
Bio/LiveSeq/Prim_Transcript.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Prim_Transcript.pm \
Bio/SeqIO/game/gameSubs.pm \
$(INST_LIBDIR)/Bio/SeqIO/game/gameSubs.pm \
Bio/Tools/Run/StandAloneBlast.pm \
$(INST_LIBDIR)/Bio/Tools/Run/StandAloneBlast.pm \
Bio/Symbol/Symbol.pm \
$(INST_LIBDIR)/Bio/Symbol/Symbol.pm \
Bio/Biblio/IO.pm \
$(INST_LIBDIR)/Bio/Biblio/IO.pm \
Bio/Factory/DriverFactory.pm \
$(INST_LIBDIR)/Bio/Factory/DriverFactory.pm \
Bio/PopGen/IO/csv.pm \
$(INST_LIBDIR)/Bio/PopGen/IO/csv.pm \
Bio/Tree/Tree.pm \
$(INST_LIBDIR)/Bio/Tree/Tree.pm \
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm \
$(INST_LIBDIR)/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm \
Bio/Tools/Analysis/Protein/Domcut.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Domcut.pm \
Bio/Graphics/Glyph/primers.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/primers.pm \
Bio/Tools/Analysis/Protein/Mitoprot.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Mitoprot.pm \
Bio/SeqIO/game/gameWriter.pm \
$(INST_LIBDIR)/Bio/SeqIO/game/gameWriter.pm \
Bio/Tools/Prediction/Exon.pm \
$(INST_LIBDIR)/Bio/Tools/Prediction/Exon.pm \
Bio/SearchIO/wise.pm \
$(INST_LIBDIR)/Bio/SearchIO/wise.pm \
Bio/Phenotype/OMIM/MiniMIMentry.pm \
$(INST_LIBDIR)/Bio/Phenotype/OMIM/MiniMIMentry.pm \
Bio/SimpleAnalysisI.pm \
$(INST_LIBDIR)/Bio/SimpleAnalysisI.pm \
Bio/Graphics/Glyph/crossbox.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/crossbox.pm \
Bio/Tools/Blast/HSP.pm \
$(INST_LIBDIR)/Bio/Tools/Blast/HSP.pm \
Bio/Seq/Meta.pm \
$(INST_LIBDIR)/Bio/Seq/Meta.pm \
Bio/SeqFeature/AnnotationAdaptor.pm \
$(INST_LIBDIR)/Bio/SeqFeature/AnnotationAdaptor.pm \
Bio/Tools/SeqStats.pm \
$(INST_LIBDIR)/Bio/Tools/SeqStats.pm \
Bio/LiveSeq/ChainI.pm \
$(INST_LIBDIR)/Bio/LiveSeq/ChainI.pm \
Bio/Variation/SeqDiff.pm \
$(INST_LIBDIR)/Bio/Variation/SeqDiff.pm \
Bio/SeqFeature/SiRNA/Oligo.pm \
$(INST_LIBDIR)/Bio/SeqFeature/SiRNA/Oligo.pm \
Bio/Search/Hit/BlastHit.pm \
$(INST_LIBDIR)/Bio/Search/Hit/BlastHit.pm \
Bio/Assembly/Scaffold.pm \
$(INST_LIBDIR)/Bio/Assembly/Scaffold.pm \
Bio/Tools/Primer3.pm \
$(INST_LIBDIR)/Bio/Tools/Primer3.pm \
Bio/Matrix/Generic.pm \
$(INST_LIBDIR)/Bio/Matrix/Generic.pm \
Bio/SearchIO/blastxml.pm \
$(INST_LIBDIR)/Bio/SearchIO/blastxml.pm \
Bio/UpdateableSeqI.pm \
$(INST_LIBDIR)/Bio/UpdateableSeqI.pm \
Bio/Restriction/IO.pm \
$(INST_LIBDIR)/Bio/Restriction/IO.pm \
Bio/SeqFeature/Gene/Exon.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/Exon.pm \
Bio/Map/MarkerI.pm \
$(INST_LIBDIR)/Bio/Map/MarkerI.pm \
Bio/Matrix/IO/phylip.pm \
$(INST_LIBDIR)/Bio/Matrix/IO/phylip.pm \
Bio/DB/BiblioI.pm \
$(INST_LIBDIR)/Bio/DB/BiblioI.pm \
Bio/SearchIO/waba.pm \
$(INST_LIBDIR)/Bio/SearchIO/waba.pm \
Bio/Species.pm \
$(INST_LIBDIR)/Bio/Species.pm \
Bio/Tools/pSW.pm \
$(INST_LIBDIR)/Bio/Tools/pSW.pm \
Bio/Coordinate/Pair.pm \
$(INST_LIBDIR)/Bio/Coordinate/Pair.pm \
Bio/IdentifiableI.pm \
$(INST_LIBDIR)/Bio/IdentifiableI.pm \
Bio/LiveSeq/IO/README \
$(INST_LIBDIR)/Bio/LiveSeq/IO/README \
Bio/Index/GenBank.pm \
$(INST_LIBDIR)/Bio/Index/GenBank.pm \
Bio/AlignIO/stockholm.pm \
$(INST_LIBDIR)/Bio/AlignIO/stockholm.pm \
Bio/LiveSeq/IO/BioPerl.pm \
$(INST_LIBDIR)/Bio/LiveSeq/IO/BioPerl.pm \
Bio/Ontology/GOterm.pm \
$(INST_LIBDIR)/Bio/Ontology/GOterm.pm \
Bio/Tools/Seg.pm \
$(INST_LIBDIR)/Bio/Tools/Seg.pm \
Bio/Tools/AlignFactory.pm \
$(INST_LIBDIR)/Bio/Tools/AlignFactory.pm \
Bio/DB/Taxonomy/entrez.pm \
$(INST_LIBDIR)/Bio/DB/Taxonomy/entrez.pm \
Bio/SearchIO/sim4.pm \
$(INST_LIBDIR)/Bio/SearchIO/sim4.pm \
Bio/OntologyIO/simplehierarchy.pm \
$(INST_LIBDIR)/Bio/OntologyIO/simplehierarchy.pm \
Bio/SeqFeature/Gene/Intron.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/Intron.pm \
Bio/Search/HSP/BlastHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/BlastHSP.pm \
Bio/DB/Flat/BDB/swiss.pm \
$(INST_LIBDIR)/Bio/DB/Flat/BDB/swiss.pm \
Bio/Tools/Promoterwise.pm \
$(INST_LIBDIR)/Bio/Tools/Promoterwise.pm \
Bio/Map/MapI.pm \
$(INST_LIBDIR)/Bio/Map/MapI.pm \
Bio/Tools/Phylo/PAML/ModelResult.pm \
$(INST_LIBDIR)/Bio/Tools/Phylo/PAML/ModelResult.pm \
Bio/Location/Atomic.pm \
$(INST_LIBDIR)/Bio/Location/Atomic.pm \
Bio/Root/Utilities.pm \
$(INST_LIBDIR)/Bio/Root/Utilities.pm \
Bio/Graphics/Glyph/pinsertion.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/pinsertion.pm \
Bio/SeqIO/genbank.pm \
$(INST_LIBDIR)/Bio/SeqIO/genbank.pm \
Bio/PopGen/IO.pm \
$(INST_LIBDIR)/Bio/PopGen/IO.pm \
Bio/Matrix/IO/scoring.pm \
$(INST_LIBDIR)/Bio/Matrix/IO/scoring.pm \
Bio/Graphics/Glyph/arrow.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/arrow.pm \
Bio/Biblio/Service.pm \
$(INST_LIBDIR)/Bio/Biblio/Service.pm \
Bio/Map/Microsatellite.pm \
$(INST_LIBDIR)/Bio/Map/Microsatellite.pm \
Bio/Tools/Primer/Pair.pm \
$(INST_LIBDIR)/Bio/Tools/Primer/Pair.pm \
Bio/DB/GFF/Featname.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Featname.pm \
Bio/SearchIO/Writer/HitTableWriter.pm \
$(INST_LIBDIR)/Bio/SearchIO/Writer/HitTableWriter.pm \
Bio/Tools/EPCR.pm \
$(INST_LIBDIR)/Bio/Tools/EPCR.pm \
Bio/Graphics/Glyph/line.pm \
$(INST_LIBDIR)/Bio/Graphics/Glyph/line.pm \
Bio/SeqFeature/Gene/ExonI.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Gene/ExonI.pm \
Bio/DB/Flat.pm \
$(INST_LIBDIR)/Bio/DB/Flat.pm \
Bio/Assembly/IO/phrap.pm \
$(INST_LIBDIR)/Bio/Assembly/IO/phrap.pm \
Bio/Taxonomy/Tree.pm \
$(INST_LIBDIR)/Bio/Taxonomy/Tree.pm \
Bio/Location/Fuzzy.pm \
$(INST_LIBDIR)/Bio/Location/Fuzzy.pm \
Bio/Index/Blast.pm \
$(INST_LIBDIR)/Bio/Index/Blast.pm \
Bio/SeqFeature/Collection.pm \
$(INST_LIBDIR)/Bio/SeqFeature/Collection.pm \
Bio/Tools/Analysis/DNA/ESEfinder.pm \
$(INST_LIBDIR)/Bio/Tools/Analysis/DNA/ESEfinder.pm \
Bio/TreeIO/newick.pm \
$(INST_LIBDIR)/Bio/TreeIO/newick.pm \
Bio/SeqIO/MultiFile.pm \
$(INST_LIBDIR)/Bio/SeqIO/MultiFile.pm \
Bio/Tools/RestrictionEnzyme.pm \
$(INST_LIBDIR)/Bio/Tools/RestrictionEnzyme.pm \
Bio/Tools/Primer/Assessor/Base.pm \
$(INST_LIBDIR)/Bio/Tools/Primer/Assessor/Base.pm \
Bio/Search/HSP/FastaHSP.pm \
$(INST_LIBDIR)/Bio/Search/HSP/FastaHSP.pm \
Bio/Map/PositionI.pm \
$(INST_LIBDIR)/Bio/Map/PositionI.pm \
Bio/Coordinate/Result.pm \
$(INST_LIBDIR)/Bio/Coordinate/Result.pm \
Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
$(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
Bio/DB/Query/WebQuery.pm \
$(INST_LIBDIR)/Bio/DB/Query/WebQuery.pm \
Bio/Seq/SeqFactory.pm \
$(INST_LIBDIR)/Bio/Seq/SeqFactory.pm \
Bio/Root/Storable.pm \
$(INST_LIBDIR)/Bio/Root/Storable.pm \
Bio/SearchIO/fasta.pm \
$(INST_LIBDIR)/Bio/SearchIO/fasta.pm \
Bio/Root/Root.pm \
$(INST_LIBDIR)/Bio/Root/Root.pm \
Bio/Phenotype/Correlate.pm \
$(INST_LIBDIR)/Bio/Phenotype/Correlate.pm \
Bio/Tools/pICalculator.pm \
$(INST_LIBDIR)/Bio/Tools/pICalculator.pm \
Bio/Matrix/PSM/PsmI.pm \
$(INST_LIBDIR)/Bio/Matrix/PSM/PsmI.pm \
Bio/LiveSeq/Exon.pm \
$(INST_LIBDIR)/Bio/LiveSeq/Exon.pm \
Bio/PopGen/MarkerI.pm \
$(INST_LIBDIR)/Bio/PopGen/MarkerI.pm
# --- MakeMaker tool_autosplit section:
# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
AUTOSPLITFILE = $(PERL) "-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" -e 'use AutoSplit;autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1) ;'
# --- MakeMaker tool_xsubpp section:
# --- MakeMaker tools_other section:
SHELL = /bin/sh
CHMOD = chmod
CP = cp
LD = ld
MV = mv
NOOP = $(SHELL) -c true
RM_F = rm -f
RM_RF = rm -rf
TEST_F = test -f
TOUCH = touch
UMASK_NULL = umask 0
DEV_NULL = > /dev/null 2>&1
# The following is a portable way to say mkdir -p
# To see which directories are created, change the if 0 to if 1
MKPATH = $(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Command -e mkpath
# This helps us to minimize the effect of the .exists files A yet
# better solution would be to have a stable file in the perl
# distribution with a timestamp of zero. But this solution doesn't
# need any changes to the core distribution and works with older perls
EQUALIZE_TIMESTAMP = $(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Command -e eqtime
# Here we warn users that an old packlist file was found somewhere,
# and that they should call some uninstall routine
WARN_IF_OLD_PACKLIST = $(PERL) -we 'exit unless -f $$ARGV[0];' \
-e 'print "WARNING: I have found an old package in\n";' \
-e 'print "\t$$ARGV[0].\n";' \
-e 'print "Please make sure the two installations are not conflicting\n";'
UNINST=0
VERBINST=1
MOD_INSTALL = $(PERL) -I$(INST_LIB) -I$(PERL_LIB) -MExtUtils::Install \
-e "install({@ARGV},'$(VERBINST)',0,'$(UNINST)');"
DOC_INSTALL = $(PERL) -e '$$\="\n\n";' \
-e 'print "=head2 ", scalar(localtime), ": C<", shift, ">", " L<", shift, ">";' \
-e 'print "=over 4";' \
-e 'while (defined($$key = shift) and defined($$val = shift)){print "=item *";print "C<$$key: $$val>";}' \
-e 'print "=back";'
UNINSTALL = $(PERL) -MExtUtils::Install \
-e 'uninstall($$ARGV[0],1,1); print "\nUninstall is deprecated. Please check the";' \
-e 'print " packlist above carefully.\n There may be errors. Remove the";' \
-e 'print " appropriate files manually.\n Sorry for the inconveniences.\n"'
# --- MakeMaker dist section:
DISTVNAME = $(DISTNAME)-$(VERSION)
TAR = tar
TARFLAGS = cvf
ZIP = zip
ZIPFLAGS = -r
COMPRESS = gzip -9f
SUFFIX = .gz
SHAR = shar
PREOP = @$(NOOP)
POSTOP = @$(NOOP)
TO_UNIX = @$(NOOP)
CI = ci -u
RCS_LABEL = rcs -Nv$(VERSION_SYM): -q
DIST_CP = best
DIST_DEFAULT = all tardist
# --- MakeMaker macro section:
# --- MakeMaker depend section:
# --- MakeMaker cflags section:
# --- MakeMaker const_loadlibs section:
# --- MakeMaker const_cccmd section:
# --- MakeMaker post_constants section:
# --- MakeMaker pasthru section:
PASTHRU = LIB="$(LIB)"\
LIBPERL_A="$(LIBPERL_A)"\
LINKTYPE="$(LINKTYPE)"\
PREFIX="$(PREFIX)"\
OPTIMIZE="$(OPTIMIZE)"
# --- MakeMaker c_o section:
# --- MakeMaker xs_c section:
# --- MakeMaker xs_o section:
# --- MakeMaker top_targets section:
#all :: config $(INST_PM) subdirs linkext manifypods
all :: pure_all htmlifypods manifypods
@$(NOOP)
pure_all :: config pm_to_blib subdirs linkext
@$(NOOP)
subdirs :: $(MYEXTLIB)
@$(NOOP)
config :: Makefile $(INST_LIBDIR)/.exists
@$(NOOP)
config :: $(INST_ARCHAUTODIR)/.exists
@$(NOOP)
config :: $(INST_AUTODIR)/.exists
@$(NOOP)
$(INST_AUTODIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
@$(MKPATH) $(INST_AUTODIR)
@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_AUTODIR)/.exists
-@$(CHMOD) $(PERM_RWX) $(INST_AUTODIR)
$(INST_LIBDIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
@$(MKPATH) $(INST_LIBDIR)
@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_LIBDIR)/.exists
-@$(CHMOD) $(PERM_RWX) $(INST_LIBDIR)
$(INST_ARCHAUTODIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
@$(MKPATH) $(INST_ARCHAUTODIR)
@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_ARCHAUTODIR)/.exists
-@$(CHMOD) $(PERM_RWX) $(INST_ARCHAUTODIR)
config :: $(INST_MAN1DIR)/.exists
@$(NOOP)
$(INST_MAN1DIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
@$(MKPATH) $(INST_MAN1DIR)
@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_MAN1DIR)/.exists
-@$(CHMOD) $(PERM_RWX) $(INST_MAN1DIR)
config :: $(INST_MAN3DIR)/.exists
@$(NOOP)
$(INST_MAN3DIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
@$(MKPATH) $(INST_MAN3DIR)
@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_MAN3DIR)/.exists
-@$(CHMOD) $(PERM_RWX) $(INST_MAN3DIR)
help:
perldoc ExtUtils::MakeMaker
Version_check:
@$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) \
-MExtUtils::MakeMaker=Version_check \
-e "Version_check('$(MM_VERSION)')"
# --- MakeMaker linkext section:
linkext :: $(LINKTYPE)
@$(NOOP)
# --- MakeMaker dlsyms section:
# --- MakeMaker dynamic section:
## $(INST_PM) has been moved to the all: target.
## It remains here for awhile to allow for old usage: "make dynamic"
#dynamic :: Makefile $(INST_DYNAMIC) $(INST_BOOT) $(INST_PM)
dynamic :: Makefile $(INST_DYNAMIC) $(INST_BOOT)
@$(NOOP)
# --- MakeMaker dynamic_bs section:
BOOTSTRAP =
# --- MakeMaker dynamic_lib section:
# --- MakeMaker static section:
## $(INST_PM) has been moved to the all: target.
## It remains here for awhile to allow for old usage: "make static"
#static :: Makefile $(INST_STATIC) $(INST_PM)
static :: Makefile $(INST_STATIC)
@$(NOOP)
# --- MakeMaker static_lib section:
# --- MakeMaker htmlifypods section:
htmlifypods : pure_all
@$(NOOP)
# --- MakeMaker manifypods section:
manifypods : pure_all
@$(NOOP)
# --- MakeMaker processPL section:
all :: bioscripts.pod
@$(NOOP)
bioscripts.pod :: doc/makedoc.PL
$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL bioscripts.pod
all :: biodatabases.pod
@$(NOOP)
biodatabases.pod :: doc/makedoc.PL
$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL biodatabases.pod
all :: biodesign.pod
@$(NOOP)
biodesign.pod :: doc/makedoc.PL
$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL biodesign.pod
all :: bioperl.pod
@$(NOOP)
bioperl.pod :: doc/makedoc.PL
$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL bioperl.pod
# --- MakeMaker installbin section:
$(INST_SCRIPT)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h
@$(MKPATH) $(INST_SCRIPT)
@$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_SCRIPT)/.exists
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)
EXE_FILES = ./scripts_temp/bp_load_gff.pl ./scripts_temp/bp_genbank2gff.pl ./scripts_temp/bp_bulk_load_gff.pl ./scripts_temp/bp_fast_load_gff.pl ./scripts_temp/bp_generate_histogram.pl ./scripts_temp/bp_pg_bulk_load_gff.pl ./scripts_temp/bp_process_gadfly.pl ./scripts_temp/bp_process_ncbi_human.pl ./scripts_temp/bp_process_sgd.pl ./scripts_temp/bp_process_wormbase.pl ./scripts_temp/bp_biofetch_genbank_proxy.pl ./scripts_temp/bp_bioflat_index.pl ./scripts_temp/bp_biogetseq.pl ./scripts_temp/bp_flanks.pl ./scripts_temp/bp_biblio.pl ./scripts_temp/bp_frend.pl ./scripts_temp/bp_feature_draw.pl ./scripts_temp/bp_search_overview.pl ./scripts_temp/bp_fetch.pl ./scripts_temp/bp_index.pl ./scripts_temp/bp_composite_LD.pl ./scripts_temp/bp_heterogeneity_test.pl ./scripts_temp/bp_filter_search.pl ./scripts_temp/bp_extract_feature_seq.pl ./scripts_temp/bp_seqconvert.pl ./scripts_temp/bp_split_seq.pl ./scripts_temp/bp_translate_seq.pl ./scripts_temp/bp_aacomp.pl ./scripts_temp/bp_chaos_plot.pl ./scripts_temp/bp_gccalc.pl ./scripts_temp/bp_oligo_count.pl ./scripts_temp/bp_local_taxonomydb_query.pl ./scripts_temp/bp_taxid4species.pl ./scripts_temp/bp_blast2tree.pl ./scripts_temp/bp_nrdb.pl ./scripts_temp/bp_mrtrans.pl ./scripts_temp/bp_sreformat.pl ./scripts_temp/bp_dbsplit.pl ./scripts_temp/bp_mask_by_search.pl ./scripts_temp/bp_mutate.pl ./scripts_temp/bp_pairwise_kaks.pl ./scripts_temp/bp_remote_blast.pl ./scripts_temp/bp_search2BSML.pl ./scripts_temp/bp_search2alnblocks.pl ./scripts_temp/bp_search2gff.pl ./scripts_temp/bp_search2tribe.pl ./scripts_temp/bp_seq_length.pl
FIXIN = $(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::MakeMaker \
-e "MY->fixin(shift)"
pure_all :: $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_sreformat.pl $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_biogetseq.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_index.pl $(INST_SCRIPT)/bp_split_seq.pl $(INST_SCRIPT)/bp_remote_blast.pl $(INST_SCRIPT)/bp_aacomp.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_frend.pl $(INST_SCRIPT)/bp_generate_histogram.pl $(INST_SCRIPT)/bp_process_sgd.pl $(INST_SCRIPT)/bp_mutate.pl $(INST_SCRIPT)/bp_filter_search.pl $(INST_SCRIPT)/bp_genbank2gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_nrdb.pl $(INST_SCRIPT)/bp_blast2tree.pl
@$(NOOP)
realclean ::
rm -f $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_sreformat.pl $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_biogetseq.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_index.pl $(INST_SCRIPT)/bp_split_seq.pl $(INST_SCRIPT)/bp_remote_blast.pl $(INST_SCRIPT)/bp_aacomp.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_frend.pl $(INST_SCRIPT)/bp_generate_histogram.pl $(INST_SCRIPT)/bp_process_sgd.pl $(INST_SCRIPT)/bp_mutate.pl $(INST_SCRIPT)/bp_filter_search.pl $(INST_SCRIPT)/bp_genbank2gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_nrdb.pl $(INST_SCRIPT)/bp_blast2tree.pl
$(INST_SCRIPT)/bp_chaos_plot.pl: ./scripts_temp/bp_chaos_plot.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_chaos_plot.pl
cp ./scripts_temp/bp_chaos_plot.pl $(INST_SCRIPT)/bp_chaos_plot.pl
$(FIXIN) $(INST_SCRIPT)/bp_chaos_plot.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_chaos_plot.pl
$(INST_SCRIPT)/bp_composite_LD.pl: ./scripts_temp/bp_composite_LD.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_composite_LD.pl
cp ./scripts_temp/bp_composite_LD.pl $(INST_SCRIPT)/bp_composite_LD.pl
$(FIXIN) $(INST_SCRIPT)/bp_composite_LD.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_composite_LD.pl
$(INST_SCRIPT)/bp_pairwise_kaks.pl: ./scripts_temp/bp_pairwise_kaks.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_pairwise_kaks.pl
cp ./scripts_temp/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl
$(FIXIN) $(INST_SCRIPT)/bp_pairwise_kaks.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_pairwise_kaks.pl
$(INST_SCRIPT)/bp_flanks.pl: ./scripts_temp/bp_flanks.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_flanks.pl
cp ./scripts_temp/bp_flanks.pl $(INST_SCRIPT)/bp_flanks.pl
$(FIXIN) $(INST_SCRIPT)/bp_flanks.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_flanks.pl
$(INST_SCRIPT)/bp_translate_seq.pl: ./scripts_temp/bp_translate_seq.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_translate_seq.pl
cp ./scripts_temp/bp_translate_seq.pl $(INST_SCRIPT)/bp_translate_seq.pl
$(FIXIN) $(INST_SCRIPT)/bp_translate_seq.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_translate_seq.pl
$(INST_SCRIPT)/bp_feature_draw.pl: ./scripts_temp/bp_feature_draw.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_feature_draw.pl
cp ./scripts_temp/bp_feature_draw.pl $(INST_SCRIPT)/bp_feature_draw.pl
$(FIXIN) $(INST_SCRIPT)/bp_feature_draw.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_feature_draw.pl
$(INST_SCRIPT)/bp_load_gff.pl: ./scripts_temp/bp_load_gff.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_load_gff.pl
cp ./scripts_temp/bp_load_gff.pl $(INST_SCRIPT)/bp_load_gff.pl
$(FIXIN) $(INST_SCRIPT)/bp_load_gff.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_load_gff.pl
$(INST_SCRIPT)/bp_biblio.pl: ./scripts_temp/bp_biblio.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_biblio.pl
cp ./scripts_temp/bp_biblio.pl $(INST_SCRIPT)/bp_biblio.pl
$(FIXIN) $(INST_SCRIPT)/bp_biblio.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biblio.pl
$(INST_SCRIPT)/bp_fast_load_gff.pl: ./scripts_temp/bp_fast_load_gff.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_fast_load_gff.pl
cp ./scripts_temp/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_fast_load_gff.pl
$(FIXIN) $(INST_SCRIPT)/bp_fast_load_gff.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_fast_load_gff.pl
$(INST_SCRIPT)/bp_search_overview.pl: ./scripts_temp/bp_search_overview.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_search_overview.pl
cp ./scripts_temp/bp_search_overview.pl $(INST_SCRIPT)/bp_search_overview.pl
$(FIXIN) $(INST_SCRIPT)/bp_search_overview.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search_overview.pl
$(INST_SCRIPT)/bp_search2tribe.pl: ./scripts_temp/bp_search2tribe.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_search2tribe.pl
cp ./scripts_temp/bp_search2tribe.pl $(INST_SCRIPT)/bp_search2tribe.pl
$(FIXIN) $(INST_SCRIPT)/bp_search2tribe.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2tribe.pl
$(INST_SCRIPT)/bp_fetch.pl: ./scripts_temp/bp_fetch.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_fetch.pl
cp ./scripts_temp/bp_fetch.pl $(INST_SCRIPT)/bp_fetch.pl
$(FIXIN) $(INST_SCRIPT)/bp_fetch.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_fetch.pl
$(INST_SCRIPT)/bp_seq_length.pl: ./scripts_temp/bp_seq_length.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_seq_length.pl
cp ./scripts_temp/bp_seq_length.pl $(INST_SCRIPT)/bp_seq_length.pl
$(FIXIN) $(INST_SCRIPT)/bp_seq_length.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_seq_length.pl
$(INST_SCRIPT)/bp_search2gff.pl: ./scripts_temp/bp_search2gff.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_search2gff.pl
cp ./scripts_temp/bp_search2gff.pl $(INST_SCRIPT)/bp_search2gff.pl
$(FIXIN) $(INST_SCRIPT)/bp_search2gff.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2gff.pl
$(INST_SCRIPT)/bp_extract_feature_seq.pl: ./scripts_temp/bp_extract_feature_seq.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_extract_feature_seq.pl
cp ./scripts_temp/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl
$(FIXIN) $(INST_SCRIPT)/bp_extract_feature_seq.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_extract_feature_seq.pl
$(INST_SCRIPT)/bp_pg_bulk_load_gff.pl: ./scripts_temp/bp_pg_bulk_load_gff.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
cp ./scripts_temp/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
$(FIXIN) $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl
$(INST_SCRIPT)/bp_sreformat.pl: ./scripts_temp/bp_sreformat.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_sreformat.pl
cp ./scripts_temp/bp_sreformat.pl $(INST_SCRIPT)/bp_sreformat.pl
$(FIXIN) $(INST_SCRIPT)/bp_sreformat.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_sreformat.pl
$(INST_SCRIPT)/bp_dbsplit.pl: ./scripts_temp/bp_dbsplit.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_dbsplit.pl
cp ./scripts_temp/bp_dbsplit.pl $(INST_SCRIPT)/bp_dbsplit.pl
$(FIXIN) $(INST_SCRIPT)/bp_dbsplit.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_dbsplit.pl
$(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl: ./scripts_temp/bp_biofetch_genbank_proxy.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
cp ./scripts_temp/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
$(FIXIN) $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl
$(INST_SCRIPT)/bp_bioflat_index.pl: ./scripts_temp/bp_bioflat_index.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_bioflat_index.pl
cp ./scripts_temp/bp_bioflat_index.pl $(INST_SCRIPT)/bp_bioflat_index.pl
$(FIXIN) $(INST_SCRIPT)/bp_bioflat_index.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_bioflat_index.pl
$(INST_SCRIPT)/bp_search2alnblocks.pl: ./scripts_temp/bp_search2alnblocks.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_search2alnblocks.pl
cp ./scripts_temp/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_search2alnblocks.pl
$(FIXIN) $(INST_SCRIPT)/bp_search2alnblocks.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2alnblocks.pl
$(INST_SCRIPT)/bp_local_taxonomydb_query.pl: ./scripts_temp/bp_local_taxonomydb_query.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
cp ./scripts_temp/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
$(FIXIN) $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_local_taxonomydb_query.pl
$(INST_SCRIPT)/bp_biogetseq.pl: ./scripts_temp/bp_biogetseq.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_biogetseq.pl
cp ./scripts_temp/bp_biogetseq.pl $(INST_SCRIPT)/bp_biogetseq.pl
$(FIXIN) $(INST_SCRIPT)/bp_biogetseq.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biogetseq.pl
$(INST_SCRIPT)/bp_process_wormbase.pl: ./scripts_temp/bp_process_wormbase.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_process_wormbase.pl
cp ./scripts_temp/bp_process_wormbase.pl $(INST_SCRIPT)/bp_process_wormbase.pl
$(FIXIN) $(INST_SCRIPT)/bp_process_wormbase.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_wormbase.pl
$(INST_SCRIPT)/bp_search2BSML.pl: ./scripts_temp/bp_search2BSML.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_search2BSML.pl
cp ./scripts_temp/bp_search2BSML.pl $(INST_SCRIPT)/bp_search2BSML.pl
$(FIXIN) $(INST_SCRIPT)/bp_search2BSML.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2BSML.pl
$(INST_SCRIPT)/bp_taxid4species.pl: ./scripts_temp/bp_taxid4species.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_taxid4species.pl
cp ./scripts_temp/bp_taxid4species.pl $(INST_SCRIPT)/bp_taxid4species.pl
$(FIXIN) $(INST_SCRIPT)/bp_taxid4species.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_taxid4species.pl
$(INST_SCRIPT)/bp_mask_by_search.pl: ./scripts_temp/bp_mask_by_search.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_mask_by_search.pl
cp ./scripts_temp/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mask_by_search.pl
$(FIXIN) $(INST_SCRIPT)/bp_mask_by_search.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mask_by_search.pl
$(INST_SCRIPT)/bp_mrtrans.pl: ./scripts_temp/bp_mrtrans.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_mrtrans.pl
cp ./scripts_temp/bp_mrtrans.pl $(INST_SCRIPT)/bp_mrtrans.pl
$(FIXIN) $(INST_SCRIPT)/bp_mrtrans.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mrtrans.pl
$(INST_SCRIPT)/bp_process_gadfly.pl: ./scripts_temp/bp_process_gadfly.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_process_gadfly.pl
cp ./scripts_temp/bp_process_gadfly.pl $(INST_SCRIPT)/bp_process_gadfly.pl
$(FIXIN) $(INST_SCRIPT)/bp_process_gadfly.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_gadfly.pl
$(INST_SCRIPT)/bp_gccalc.pl: ./scripts_temp/bp_gccalc.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_gccalc.pl
cp ./scripts_temp/bp_gccalc.pl $(INST_SCRIPT)/bp_gccalc.pl
$(FIXIN) $(INST_SCRIPT)/bp_gccalc.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_gccalc.pl
$(INST_SCRIPT)/bp_seqconvert.pl: ./scripts_temp/bp_seqconvert.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_seqconvert.pl
cp ./scripts_temp/bp_seqconvert.pl $(INST_SCRIPT)/bp_seqconvert.pl
$(FIXIN) $(INST_SCRIPT)/bp_seqconvert.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_seqconvert.pl
$(INST_SCRIPT)/bp_oligo_count.pl: ./scripts_temp/bp_oligo_count.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_oligo_count.pl
cp ./scripts_temp/bp_oligo_count.pl $(INST_SCRIPT)/bp_oligo_count.pl
$(FIXIN) $(INST_SCRIPT)/bp_oligo_count.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_oligo_count.pl
$(INST_SCRIPT)/bp_process_ncbi_human.pl: ./scripts_temp/bp_process_ncbi_human.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_process_ncbi_human.pl
cp ./scripts_temp/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl
$(FIXIN) $(INST_SCRIPT)/bp_process_ncbi_human.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_ncbi_human.pl
$(INST_SCRIPT)/bp_index.pl: ./scripts_temp/bp_index.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_index.pl
cp ./scripts_temp/bp_index.pl $(INST_SCRIPT)/bp_index.pl
$(FIXIN) $(INST_SCRIPT)/bp_index.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_index.pl
$(INST_SCRIPT)/bp_split_seq.pl: ./scripts_temp/bp_split_seq.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_split_seq.pl
cp ./scripts_temp/bp_split_seq.pl $(INST_SCRIPT)/bp_split_seq.pl
$(FIXIN) $(INST_SCRIPT)/bp_split_seq.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_split_seq.pl
$(INST_SCRIPT)/bp_remote_blast.pl: ./scripts_temp/bp_remote_blast.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_remote_blast.pl
cp ./scripts_temp/bp_remote_blast.pl $(INST_SCRIPT)/bp_remote_blast.pl
$(FIXIN) $(INST_SCRIPT)/bp_remote_blast.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_remote_blast.pl
$(INST_SCRIPT)/bp_aacomp.pl: ./scripts_temp/bp_aacomp.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_aacomp.pl
cp ./scripts_temp/bp_aacomp.pl $(INST_SCRIPT)/bp_aacomp.pl
$(FIXIN) $(INST_SCRIPT)/bp_aacomp.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_aacomp.pl
$(INST_SCRIPT)/bp_heterogeneity_test.pl: ./scripts_temp/bp_heterogeneity_test.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_heterogeneity_test.pl
cp ./scripts_temp/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl
$(FIXIN) $(INST_SCRIPT)/bp_heterogeneity_test.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_heterogeneity_test.pl
$(INST_SCRIPT)/bp_frend.pl: ./scripts_temp/bp_frend.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_frend.pl
cp ./scripts_temp/bp_frend.pl $(INST_SCRIPT)/bp_frend.pl
$(FIXIN) $(INST_SCRIPT)/bp_frend.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_frend.pl
$(INST_SCRIPT)/bp_generate_histogram.pl: ./scripts_temp/bp_generate_histogram.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_generate_histogram.pl
cp ./scripts_temp/bp_generate_histogram.pl $(INST_SCRIPT)/bp_generate_histogram.pl
$(FIXIN) $(INST_SCRIPT)/bp_generate_histogram.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_generate_histogram.pl
$(INST_SCRIPT)/bp_process_sgd.pl: ./scripts_temp/bp_process_sgd.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_process_sgd.pl
cp ./scripts_temp/bp_process_sgd.pl $(INST_SCRIPT)/bp_process_sgd.pl
$(FIXIN) $(INST_SCRIPT)/bp_process_sgd.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_sgd.pl
$(INST_SCRIPT)/bp_mutate.pl: ./scripts_temp/bp_mutate.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_mutate.pl
cp ./scripts_temp/bp_mutate.pl $(INST_SCRIPT)/bp_mutate.pl
$(FIXIN) $(INST_SCRIPT)/bp_mutate.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mutate.pl
$(INST_SCRIPT)/bp_filter_search.pl: ./scripts_temp/bp_filter_search.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_filter_search.pl
cp ./scripts_temp/bp_filter_search.pl $(INST_SCRIPT)/bp_filter_search.pl
$(FIXIN) $(INST_SCRIPT)/bp_filter_search.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_filter_search.pl
$(INST_SCRIPT)/bp_genbank2gff.pl: ./scripts_temp/bp_genbank2gff.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_genbank2gff.pl
cp ./scripts_temp/bp_genbank2gff.pl $(INST_SCRIPT)/bp_genbank2gff.pl
$(FIXIN) $(INST_SCRIPT)/bp_genbank2gff.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_genbank2gff.pl
$(INST_SCRIPT)/bp_bulk_load_gff.pl: ./scripts_temp/bp_bulk_load_gff.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_bulk_load_gff.pl
cp ./scripts_temp/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl
$(FIXIN) $(INST_SCRIPT)/bp_bulk_load_gff.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_bulk_load_gff.pl
$(INST_SCRIPT)/bp_nrdb.pl: ./scripts_temp/bp_nrdb.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_nrdb.pl
cp ./scripts_temp/bp_nrdb.pl $(INST_SCRIPT)/bp_nrdb.pl
$(FIXIN) $(INST_SCRIPT)/bp_nrdb.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_nrdb.pl
$(INST_SCRIPT)/bp_blast2tree.pl: ./scripts_temp/bp_blast2tree.pl Makefile $(INST_SCRIPT)/.exists
@rm -f $(INST_SCRIPT)/bp_blast2tree.pl
cp ./scripts_temp/bp_blast2tree.pl $(INST_SCRIPT)/bp_blast2tree.pl
$(FIXIN) $(INST_SCRIPT)/bp_blast2tree.pl
-@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_blast2tree.pl
# --- MakeMaker subdirs section:
# none
# --- MakeMaker clean section:
# Delete temporary files but do not touch installed files. We don't delete
# the Makefile here so a later make realclean still has a makefile to use.
clean ::
-rm -rf ./blib $(MAKE_APERL_FILE) $(INST_ARCHAUTODIR)/extralibs.all perlmain.c mon.out core core.*perl.*.? *perl.core so_locations pm_to_blib *~ */*~ */*/*~ *$(OBJ_EXT) *$(LIB_EXT) perl.exe $(BOOTSTRAP) $(BASEEXT).bso $(BASEEXT).def $(BASEEXT).exp
-mv Makefile Makefile.old $(DEV_NULL)
-rm -rf scripts_temp
# --- MakeMaker realclean section:
# Delete temporary files (via clean) and also delete installed files
realclean purge :: clean
rm -rf $(INST_AUTODIR) $(INST_ARCHAUTODIR)
rm -f $(INST_LIBDIR)/Bio/SeqIO/bsml.pm $(INST_LIBDIR)/Bio/Location/NarrowestCoordPolicy.pm $(INST_LIBDIR)/Bio/MapIO.pm $(INST_LIBDIR)/Bio/SeqIO/abi.pm $(INST_LIBDIR)/Bio/OntologyIO/goflat.pm $(INST_LIBDIR)/Bio/Biblio/Organisation.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm $(INST_LIBDIR)/Bio/Taxonomy/Taxon.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/memory.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/redgreen_box.pm $(INST_LIBDIR)/Bio/Tools/PrositeScan.pm $(INST_LIBDIR)/Bio/Variation/IO.pm $(INST_LIBDIR)/Bio/Factory/FTLocationFactory.pm $(INST_LIBDIR)/Bio/Tools/ECnumber.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/HTMLResultWriter.pm $(INST_LIBDIR)/Bio/Variation/AAChange.pm $(INST_LIBDIR)/Bio/Biblio/Book.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/match.pm $(INST_LIBDIR)/Bio/Event/EventHandlerI.pm $(INST_LIBDIR)/Bio/DB/GFF/Util/Rearrange.pm $(INST_LIBDIR)/Bio/Tools/OddCodes.pm $(INST_LIBDIR)/Bio/Factory/ObjectFactoryI.pm $(INST_LIBDIR)/Bio/Search/Hit/HitFactory.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/clone.pm $(INST_LIBDIR)/Bio/Root/Global.pm $(INST_LIBDIR)/Bio/Seq.pm $(INST_LIBDIR)/Bio/Root/Vector.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/TextResultWriter.pm $(INST_LIBDIR)/Bio/Tools/HMMER/Set.pm $(INST_LIBDIR)/Bio/SeqIO/FTHelper.pm $(INST_LIBDIR)/Bio/LiveSeq/IO/SRS.pm $(INST_LIBDIR)/Bio/SearchIO/IteratedSearchResultEventBuilder.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/HNN.pm $(INST_LIBDIR)/Bio/Tools/BPlite/HSP.pm $(INST_LIBDIR)/Bio/Tools/Sigcleave.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/BSMLResultWriter.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/pg.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/triangle.pm $(INST_LIBDIR)/Bio/Assembly/IO/ace.pm $(INST_LIBDIR)/Bio/Map/CytoMap.pm $(INST_LIBDIR)/Bio/Restriction/IO/bairoch.pm $(INST_LIBDIR)/Bio/Graphics/ConfiguratorI.pm $(INST_LIBDIR)/Bio/Structure/IO.pm $(INST_LIBDIR)/Bio/Tree/RandomFactory.pm $(INST_LIBDIR)/Bio/Factory/ObjectFactory.pm $(INST_LIBDIR)/Bio/Matrix/PSM/SiteMatrix.pm $(INST_LIBDIR)/Bio/DasI.pm $(INST_LIBDIR)/Bio/Matrix/PSM/InstanceSiteI.pm $(INST_LIBDIR)/Bio/Coordinate/ExtrapolatingPair.pm $(INST_LIBDIR)/Bio/SeqIO/pir.pm $(INST_LIBDIR)/Bio/Tools/SeqAnal.pm $(INST_LIBDIR)/Bio/Annotation/StructuredValue.pm $(INST_LIBDIR)/Bio/Biblio/Ref.pm $(INST_LIBDIR)/Bio/SeqIO/phd.pm $(INST_LIBDIR)/Bio/Tools/Glimmer.pm $(INST_LIBDIR)/Bio/CodonUsage/IO.pm $(INST_LIBDIR)/Bio/Location/Simple.pm $(INST_LIBDIR)/Bio/Map/OrderedPositionWithDistance.pm $(INST_LIBDIR)/Bio/Tools/Phylo/PAML/Result.pm $(INST_LIBDIR)/Bio/AnnotationCollectionI.pm $(INST_LIBDIR)/Bio/SeqAnalysisParserI.pm $(INST_LIBDIR)/Bio/Tools/GFF.pm $(INST_LIBDIR)/Bio/Variation/AAReverseMutate.pm $(INST_LIBDIR)/Bio/Cluster/ClusterFactory.pm $(INST_LIBDIR)/Bio/Tools/SiRNA.pm $(INST_LIBDIR)/Bio/SeqIO/qual.pm $(INST_LIBDIR)/Bio/DB/EMBL.pm $(INST_LIBDIR)/Bio/Tools/SeqWords.pm $(INST_LIBDIR)/Bio/DB/UpdateableSeqI.pm $(INST_LIBDIR)/Bio/SeqFeature/Computation.pm $(INST_LIBDIR)/Bio/Matrix/IO.pm $(INST_LIBDIR)/Bio/SeqFeature/CollectionI.pm $(INST_LIBDIR)/Bio/DB/GFF/Homol.pm $(INST_LIBDIR)/Bio/SeqIO/locuslink.pm $(INST_LIBDIR)/Bio/SeqIO/ctf.pm $(INST_LIBDIR)/Bio/SeqUtils.pm $(INST_LIBDIR)/Bio/DB/Flat/BDB/embl.pm $(INST_LIBDIR)/Bio/Tools/CodonTable.pm $(INST_LIBDIR)/Bio/Variation/README $(INST_LIBDIR)/Bio/Annotation/Comment.pm $(INST_LIBDIR)/Bio/Seq/BaseSeqProcessor.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi.pm $(INST_LIBDIR)/Bio/Tools/QRNA.pm $(INST_LIBDIR)/Bio/SeqFeature/Primer.pm $(INST_LIBDIR)/Bio/PopGen/PopStats.pm $(INST_LIBDIR)/Bio/DB/SeqI.pm $(INST_LIBDIR)/Bio/Tools/Pseudowise.pm $(INST_LIBDIR)/Bio/Tools/Profile.pm $(INST_LIBDIR)/Bio/ClusterIO/unigene.pm $(INST_LIBDIR)/Bio/LiveSeq/Repeat_Region.pm $(INST_LIBDIR)/Bio/SeqFeature/Tools/TypeMapper.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator.pm $(INST_LIBDIR)/Bio/PopGen/PopulationI.pm $(INST_LIBDIR)/Bio/SeqIO/game/seqHandler.pm $(INST_LIBDIR)/Bio/AnalysisResultI.pm $(INST_LIBDIR)/Bio/Phenotype/MeSH/Term.pm $(INST_LIBDIR)/Bio/Tools/Sim4/Results.pm $(INST_LIBDIR)/Bio/Seq/PrimedSeq.pm $(INST_LIBDIR)/Bio/Biblio/MedlineJournalArticle.pm $(INST_LIBDIR)/Bio/SeqIO/swiss.pm $(INST_LIBDIR)/Bio/SeqFeatureI.pm $(INST_LIBDIR)/Bio/Biblio/BiblioBase.pm $(INST_LIBDIR)/Bio/Location/Split.pm $(INST_LIBDIR)/Bio/DB/GenPept.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/biofetch.pm $(INST_LIBDIR)/Bio/Ontology/SimpleGOEngine.pm $(INST_LIBDIR)/Bio/Graphics/Glyph.pm $(INST_LIBDIR)/Bio/Graphics/FeatureFile.pm $(INST_LIBDIR)/Bio/Tree/Node.pm $(INST_LIBDIR)/Bio/Symbol/ProteinAlphabet.pm $(INST_LIBDIR)/Bio/Tools/Prediction/Gene.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/oracleace.pm $(INST_LIBDIR)/Bio/Seq/MetaI.pm $(INST_LIBDIR)/Bio/Tools/RepeatMasker.pm $(INST_LIBDIR)/Bio/LiveSeq/Repeat_Unit.pm $(INST_LIBDIR)/Bio/Matrix/PSM/SiteMatrixI.pm $(INST_LIBDIR)/Bio/Tools/BPlite/Sbjct.pm $(INST_LIBDIR)/Bio/AnnotationI.pm $(INST_LIBDIR)/Bio/DB/XEMBL.pm $(INST_LIBDIR)/Bio/Tools/Geneid.pm $(INST_LIBDIR)/Bio/Tools/Prints.pm $(INST_LIBDIR)/Bio/Phenotype/Phenotype.pm $(INST_LIBDIR)/Bio/Tools/GuessSeqFormat.pm $(INST_LIBDIR)/Bio/Coordinate/Chain.pm $(INST_LIBDIR)/Bio/SeqIO/chadoxml.pm $(INST_LIBDIR)/Bio/Matrix/PSM/IO/mast.pm $(INST_LIBDIR)/Bio/Root/IO.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/transcript2.pm $(INST_LIBDIR)/Bio/Index/Swissprot.pm $(INST_LIBDIR)/Bio/PopGen/GenotypeI.pm $(INST_LIBDIR)/Bio/Search/HSP/PSLHSP.pm $(INST_LIBDIR)/Bio/DB/Flat/BDB/genbank.pm $(INST_LIBDIR)/Bio/DB/GFF/Util/Binning.pm $(INST_LIBDIR)/Bio/Seq/LargePrimarySeq.pm $(INST_LIBDIR)/Bio/DB/GFF.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/NC_Feature.pm $(INST_LIBDIR)/Bio/SimpleAlign.pm $(INST_LIBDIR)/Bio/SearchDist.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/alignment.pm $(INST_LIBDIR)/Bio/Symbol/Alphabet.pm $(INST_LIBDIR)/Bio/Tools/Blast/HTML.pm $(INST_LIBDIR)/Bio/Tools/Gel.pm $(INST_LIBDIR)/Bio/OntologyIO/Handlers/BaseSAXHandler.pm $(INST_LIBDIR)/Bio/Graphics/RendererI.pm $(INST_LIBDIR)/Bio/Tools/BPlite.pm $(INST_LIBDIR)/Bio/AlignIO/selex.pm $(INST_LIBDIR)/Bio/Factory/TreeFactoryI.pm $(INST_LIBDIR)/Bio/Range.pm $(INST_LIBDIR)/Bio/Matrix/Scoring.pm $(INST_LIBDIR)/Bio/Annotation/AnnotationFactory.pm $(INST_LIBDIR)/Bio/Tools/Eponine.pm $(INST_LIBDIR)/Bio/Map/Position.pm $(INST_LIBDIR)/Bio/Graphics/Util.pm $(INST_LIBDIR)/Bio/Biblio/MedlineBook.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/diamond.pm $(INST_LIBDIR)/Bio/Search/Iteration/IterationI.pm $(INST_LIBDIR)/Bio/Search/Result/GenericResult.pm $(INST_LIBDIR)/Bio/Factory/SequenceProcessorI.pm $(INST_LIBDIR)/Bio/Location/SplitLocationI.pm $(INST_LIBDIR)/Bio/SeqIO/exp.pm $(INST_LIBDIR)/Bio/Assembly/ContigAnalysis.pm $(INST_LIBDIR)/Bio/LiveSeq/DNA.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/ace.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/translation.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/ex.pm $(INST_LIBDIR)/Bio/Seq/LargeSeq.pm $(INST_LIBDIR)/Bio/Tools/Blast/README $(INST_LIBDIR)/Bio/SeqIO/metafasta.pm $(INST_LIBDIR)/Bio/Symbol/SymbolI.pm $(INST_LIBDIR)/Bio/Matrix/PSM/Psm.pm $(INST_LIBDIR)/Bio/Biblio/Thesis.pm $(INST_LIBDIR)/Bio/Search/GenericDatabase.pm $(INST_LIBDIR)/Bio/Event/EventGeneratorI.pm $(INST_LIBDIR)/Bio/Taxonomy/Node.pm $(INST_LIBDIR)/Bio/AlignIO/meme.pm $(INST_LIBDIR)/Bio/DB/GFF/Typename.pm $(INST_LIBDIR)/Bio/Coordinate/Result/Gap.pm $(INST_LIBDIR)/Bio/LiveSeq/Intron.pm $(INST_LIBDIR)/Bio/AlignIO/mase.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_refgene.pm $(INST_LIBDIR)/Bio/SeqIO/pln.pm $(INST_LIBDIR)/Bio/Structure/Atom.pm $(INST_LIBDIR)/Bio/DB/BioFetch.pm $(INST_LIBDIR)/Bio/LiveSeq/Gene.pm $(INST_LIBDIR)/Bio/Ontology/TermI.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/mysql.pm $(INST_LIBDIR)/Bio/Biblio/PubmedBookArticle.pm $(INST_LIBDIR)/Bio/SeqIO/game/featHandler.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/NetPhos.pm $(INST_LIBDIR)/Bio/SeqIO/game/gameHandler.pm $(INST_LIBDIR)/Bio/Ontology/InterProTerm.pm $(INST_LIBDIR)/Bio/Phenotype/PhenotypeI.pm $(INST_LIBDIR)/Bio/Search/Iteration/GenericIteration.pm $(INST_LIBDIR)/Bio/PopGen/Genotype.pm $(INST_LIBDIR)/Bio/Assembly/IO.pm $(INST_LIBDIR)/Bio/DB/GFF/RelSegment.pm $(INST_LIBDIR)/Bio/DB/XEMBLService.pm $(INST_LIBDIR)/Bio/SearchIO/EventHandlerI.pm $(INST_LIBDIR)/Bio/TreeIO/nhx.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/processed_transcript.pm $(INST_LIBDIR)/Bio/Ontology/TermFactory.pm $(INST_LIBDIR)/Bio/SeqI.pm $(INST_LIBDIR)/Bio/Align/StatisticsI.pm $(INST_LIBDIR)/Bio/Matrix/PSM/IO/meme.pm $(INST_LIBDIR)/Bio/Matrix/MatrixI.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/graded_segments.pm $(INST_LIBDIR)/Bio/Matrix/PhylipDist.pm $(INST_LIBDIR)/Bio/Coordinate/GeneMapper.pm $(INST_LIBDIR)/Bio/IdCollectionI.pm $(INST_LIBDIR)/Bio/Cluster/UniGene.pm $(INST_LIBDIR)/Bio/Coordinate/ResultI.pm $(INST_LIBDIR)/Bio/Ontology/Ontology.pm $(INST_LIBDIR)/Bio/Tools/Blat.pm $(INST_LIBDIR)/Bio/SeqIO/scf.pm $(INST_LIBDIR)/Bio/LiveSeq/Translation.pm $(INST_LIBDIR)/Bio/LiveSeq/Chain.pm $(INST_LIBDIR)/Bio/Seq/SeqBuilder.pm $(INST_LIBDIR)/Bio/Align/Utilities.pm $(INST_LIBDIR)/Bio/Root/Version.pm $(INST_LIBDIR)/Bio/PopGen/Marker.pm $(INST_LIBDIR)/Bio/Biblio/IO/pubmed2ref.pm $(INST_LIBDIR)/Bio/LiveSeq/Mutation.pm $(INST_LIBDIR)/Bio/Location/AvWithinCoordPolicy.pm $(INST_LIBDIR)/Bio/Tools/IUPAC.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/processed_transcript.pm $(INST_LIBDIR)/Bio/Structure/Entry.pm $(INST_LIBDIR)/Bio/Perl.pm $(INST_LIBDIR)/Bio/Align/DNAStatistics.pm $(INST_LIBDIR)/Bio/Ontology/OntologyEngineI.pm $(INST_LIBDIR)/Bio/SeqIO/ztr.pm $(INST_LIBDIR)/Bio/Tools/SeqPattern.pm $(INST_LIBDIR)/Bio/Factory/LocationFactoryI.pm $(INST_LIBDIR)/Bio/DB/CUTG.pm $(INST_LIBDIR)/Bio/SearchIO/SearchResultEventBuilder.pm $(INST_LIBDIR)/Bio/Restriction/EnzymeI.pm $(INST_LIBDIR)/Bio/SeqFeature/Tools/Unflattener.pm $(INST_LIBDIR)/Bio/ClusterI.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/Transcript.pm $(INST_LIBDIR)/Bio/Align/PairwiseStatistics.pm $(INST_LIBDIR)/Bio/Tools/WWW.pm $(INST_LIBDIR)/Bio/Tools/Tmhmm.pm $(INST_LIBDIR)/Bio/Tools/Alignment/Trim.pm $(INST_LIBDIR)/Bio/Tools/ESTScan.pm $(INST_LIBDIR)/Bio/SeqIO/asciitree.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/oval.pm $(INST_LIBDIR)/Bio/SearchIO/blasttable.pm $(INST_LIBDIR)/Bio/Tools/Primer/AssessorI.pm $(INST_LIBDIR)/Bio/Variation/IO/xml.pm $(INST_LIBDIR)/Bio/Taxonomy/FactoryI.pm $(INST_LIBDIR)/Bio/Tools/RandomDistFunctions.pm $(INST_LIBDIR)/Bio/Seq/SeqWithQuality.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/ellipse.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_genscan.pm $(INST_LIBDIR)/Bio/Biblio/MedlineArticle.pm $(INST_LIBDIR)/Bio/LiveSeq/Transcript.pm $(INST_LIBDIR)/Bio/Tools/MZEF.pm $(INST_LIBDIR)/Bio/SearchIO/hmmer.pm $(INST_LIBDIR)/Bio/Biblio/Article.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_unigene.pm $(INST_LIBDIR)/Bio/AlignIO/prodom.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/Factory.pm $(INST_LIBDIR)/Bio/Annotation/Collection.pm $(INST_LIBDIR)/Bio/Restriction/IO/itype2.pm $(INST_LIBDIR)/biodatabases.pod $(INST_LIBDIR)/Bio/Restriction/EnzymeCollection.pm $(INST_LIBDIR)/Bio/SeqIO/tab.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/Promoter.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm $(INST_LIBDIR)/Bio/Factory/SeqAnalysisParserFactoryI.pm $(INST_LIBDIR)/Bio/Graphics/Feature.pm $(INST_LIBDIR)/Bio/Restriction/IO/withrefm.pm $(INST_LIBDIR)/Bio/DB/Universal.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/anchored_arrow.pm $(INST_LIBDIR)/Bio/Tools/Grail.pm $(INST_LIBDIR)/Bio/Variation/SNP.pm $(INST_LIBDIR)/Bio/Taxonomy.pm $(INST_LIBDIR)/Bio/Variation/DNAMutation.pm $(INST_LIBDIR)/Bio/PrimarySeqI.pm $(INST_LIBDIR)/Bio/DescribableI.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/group.pm $(INST_LIBDIR)/Bio/Search/Result/ResultI.pm $(INST_LIBDIR)/Bio/Tools/Coil.pm $(INST_LIBDIR)/Bio/Expression/FeatureGroup.pm $(INST_LIBDIR)/Bio/TreeIO/tabtree.pm $(INST_LIBDIR)/Bio/Coordinate/Graph.pm $(INST_LIBDIR)/Bio/DB/Registry.pm $(INST_LIBDIR)/Bio/AnnotatableI.pm $(INST_LIBDIR)/biodesign.pod $(INST_LIBDIR)/Bio/AlignIO/psi.pm $(INST_LIBDIR)/Bio/Ontology/Term.pm $(INST_LIBDIR)/Bio/AlignIO/msf.pm $(INST_LIBDIR)/Bio/Restriction/Enzyme.pm $(INST_LIBDIR)/Bio/Coordinate/Collection.pm $(INST_LIBDIR)/Bio/Map/OrderedPosition.pm $(INST_LIBDIR)/Bio/SearchIO/megablast.pm $(INST_LIBDIR)/Bio/Search/HSP/GenericHSP.pm $(INST_LIBDIR)/Bio/Tools/Genewise.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/toomany.pm $(INST_LIBDIR)/Bio/TreeIO.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/memory_iterator.pm $(INST_LIBDIR)/Bio/Tools/Phylo/PAML.pm $(INST_LIBDIR)/Bio/DB/MeSH.pm $(INST_LIBDIR)/Bio/DB/Makefile.PL $(INST_LIBDIR)/Bio/Factory/HitFactoryI.pm $(INST_LIBDIR)/Bio/Map/CytoMarker.pm $(INST_LIBDIR)/Bio/Tree/TreeI.pm $(INST_LIBDIR)/Bio/Assembly/ScaffoldI.pm $(INST_LIBDIR)/Bio/Tree/Statistics.pm $(INST_LIBDIR)/Bio/LiveSeq/Mutator.pm $(INST_LIBDIR)/Bio/Search/BlastUtils.pm $(INST_LIBDIR)/Bio/Tools/BPlite/Iteration.pm $(INST_LIBDIR)/Bio/OntologyIO/InterProParser.pm $(INST_LIBDIR)/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm $(INST_LIBDIR)/Bio/SeqIO.pm $(INST_LIBDIR)/Bio/Index/Fasta.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/transcript.pm $(INST_LIBDIR)/bptutorial.pl $(INST_LIBDIR)/Bio/Symbol/AlphabetI.pm $(INST_LIBDIR)/Bio/SeqIO/game.pm $(INST_LIBDIR)/Bio/Biblio/MedlineBookArticle.pm $(INST_LIBDIR)/Bio/OntologyIO.pm $(INST_LIBDIR)/Bio/SeqIO/tigr.pm $(INST_LIBDIR)/Bio/AlignIO/metafasta.pm $(INST_LIBDIR)/Bio/AlignIO/pfam.pm $(INST_LIBDIR)/Bio/Map/LinkagePosition.pm $(INST_LIBDIR)/Bio/Ontology/PathI.pm $(INST_LIBDIR)/Bio/SeqIO/raw.pm $(INST_LIBDIR)/Bio/Tools/BPbl2seq.pm $(INST_LIBDIR)/Bio/Search/HSP/PsiBlastHSP.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/GeneStructureI.pm $(INST_LIBDIR)/Bio/AlignIO/bl2seq.pm $(INST_LIBDIR)/Bio/Tools/Primer/Feature.pm $(INST_LIBDIR)/Bio/Tools/Phylo/Molphy/Result.pm $(INST_LIBDIR)/Bio/Tools/Analysis/SimpleAnalysisBase.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/UTR.pm $(INST_LIBDIR)/Bio/DBLinkContainerI.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/HSPTableWriter.pm $(INST_LIBDIR)/Bio/SearchIO/axt.pm $(INST_LIBDIR)/Bio/SeqIO/kegg.pm $(INST_LIBDIR)/Bio/Tools/Genomewise.pm $(INST_LIBDIR)/Bio/DB/Ace.pm $(INST_LIBDIR)/Bio/SearchIO/psl.pm $(INST_LIBDIR)/Bio/Map/CytoPosition.pm $(INST_LIBDIR)/Bio/Index/SwissPfam.pm $(INST_LIBDIR)/Bio/Restriction/IO/base.pm $(INST_LIBDIR)/Bio/DB/Taxonomy.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/splice_site.pm $(INST_LIBDIR)/Bio/Factory/ObjectBuilderI.pm $(INST_LIBDIR)/Bio/Tools/Est2Genome.pm $(INST_LIBDIR)/Bio/AlignIO/emboss.pm $(INST_LIBDIR)/Bio/Index/Fastq.pm $(INST_LIBDIR)/Bio/DB/Flat/BDB/fasta.pm $(INST_LIBDIR)/Bio/Tools/Run/WrapperBase.pm $(INST_LIBDIR)/Bio/Annotation/Reference.pm $(INST_LIBDIR)/Bio/Biblio/PubmedArticle.pm $(INST_LIBDIR)/Bio/Root/Err.pm $(INST_LIBDIR)/Bio/Matrix/PSM/PsmHeader.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/rndrect.pm $(INST_LIBDIR)/Bio/Ontology/SimpleOntologyEngine.pm $(INST_LIBDIR)/Bio/AnalysisI.pm $(INST_LIBDIR)/Bio/Annotation/DBLink.pm $(INST_LIBDIR)/Bio/Seq/TraceI.pm $(INST_LIBDIR)/Bio/PopGen/Individual.pm $(INST_LIBDIR)/Bio/DB/Flat/BDB.pm $(INST_LIBDIR)/Bio/DB/DBFetch.pm $(INST_LIBDIR)/Bio/Seq/SequenceTrace.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/box.pm $(INST_LIBDIR)/Bio/SearchIO/SearchWriterI.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/redgreen_segment.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/span.pm $(INST_LIBDIR)/Bio/SearchIO/blast.pm $(INST_LIBDIR)/Bio/Biblio/IO/medlinexml.pm $(INST_LIBDIR)/Bio/DB/Flat/BDB/swissprot.pm $(INST_LIBDIR)/Bio/Tools/Alignment/Consed.pm $(INST_LIBDIR)/Bio/SeqFeature/Generic.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/GeneStructure.pm $(INST_LIBDIR)/Bio/Ontology/Path.pm $(INST_LIBDIR)/Bio/Tools/Run/RemoteBlast.pm $(INST_LIBDIR)/Bio/Tools/EMBOSS/Palindrome.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm $(INST_LIBDIR)/Bio/Search/SearchUtils.pm $(INST_LIBDIR)/Bio/Root/HTTPget.pm $(INST_LIBDIR)/Bio/Structure/SecStr/STRIDE/Res.pm $(INST_LIBDIR)/Bio/Map/MappableI.pm $(INST_LIBDIR)/Bio/Root/Xref.pm $(INST_LIBDIR)/Bio/Search/Hit/HMMERHit.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/minmax.pm $(INST_LIBDIR)/Bio/Symbol/README.Symbol $(INST_LIBDIR)/Bio/Graphics/Glyph/cds.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/GbrowseGFF.pm $(INST_LIBDIR)/Bio/Biblio/IO/pubmedxml.pm $(INST_LIBDIR)/Bio/Coordinate/Result/Match.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/track.pm $(INST_LIBDIR)/Bio/Root/Object.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/oracle.pm $(INST_LIBDIR)/Bio/Search/DatabaseI.pm $(INST_LIBDIR)/Bio/SeqIO/ace.pm $(INST_LIBDIR)/Bio/Location/FuzzyLocationI.pm $(INST_LIBDIR)/Bio/OntologyIO/Handlers/InterProHandler.pm $(INST_LIBDIR)/Bio/Search/Result/ResultFactory.pm $(INST_LIBDIR)/Bio/Factory/ResultFactoryI.pm $(INST_LIBDIR)/Bio/FeatureHolderI.pm $(INST_LIBDIR)/Bio/DB/QueryI.pm $(INST_LIBDIR)/Bio/Tools/AnalysisResult.pm $(INST_LIBDIR)/Bio/Biblio/BookArticle.pm $(INST_LIBDIR)/Bio/DB/MANIFEST $(INST_LIBDIR)/Bio/Matrix/PSM/PsmHeaderI.pm $(INST_LIBDIR)/Bio/Seq/RichSeqI.pm $(INST_LIBDIR)/Bio/ClusterIO/dbsnp.pm $(INST_LIBDIR)/Bio/LiveSeq/IO/Loader.pm $(INST_LIBDIR)/Bio/Variation/IO/flat.pm $(INST_LIBDIR)/Bio/CodonUsage/Table.pm $(INST_LIBDIR)/Bio/Structure/Chain.pm $(INST_LIBDIR)/Bio/LiveSeq/AARange.pm $(INST_LIBDIR)/Bio/AlignIO/mega.pm $(INST_LIBDIR)/Bio/DB/FileCache.pm $(INST_LIBDIR)/Bio/Assembly/Contig.pm $(INST_LIBDIR)/Bio/Root/RootI.pm $(INST_LIBDIR)/Bio/AnalysisParserI.pm $(INST_LIBDIR)/Bio/DB/Taxonomy/flatfile.pm $(INST_LIBDIR)/Bio/Search/HSP/HMMERHSP.pm $(INST_LIBDIR)/Bio/Tools/BPpsilite.pm $(INST_LIBDIR)/Bio/Ontology/Relationship.pm $(INST_LIBDIR)/Bio/DB/GenBank.pm $(INST_LIBDIR)/Bio/Tools/Hmmpfam.pm $(INST_LIBDIR)/Bio/Tools/Phylo/Molphy.pm $(INST_LIBDIR)/Bio/Variation/VariantI.pm $(INST_LIBDIR)/Bio/LocatableSeq.pm $(INST_LIBDIR)/Bio/Tools/Sim4/Exon.pm $(INST_LIBDIR)/Bio/OntologyIO/dagflat.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/heterogeneous_segments.pm $(INST_LIBDIR)/Bio/AlignIO/nexus.pm $(INST_LIBDIR)/Bio/Biblio/Patent.pm $(INST_LIBDIR)/Bio/Tools/Phylo/Phylip/ProtDist.pm $(INST_LIBDIR)/Bio/SeqIO/alf.pm $(INST_LIBDIR)/Bio/Location/WidestCoordPolicy.pm $(INST_LIBDIR)/Bio/DB/Query/GenBank.pm $(INST_LIBDIR)/Bio/Annotation/SimpleValue.pm $(INST_LIBDIR)/Bio/Biblio/MedlineJournal.pm $(INST_LIBDIR)/Bio/Root/IOManager.pm $(INST_LIBDIR)/Bio/OntologyIO/soflat.pm $(INST_LIBDIR)/Bio/Restriction/Enzyme/MultiCut.pm $(INST_LIBDIR)/Bio/DB/Biblio/biofetch.pm $(INST_LIBDIR)/Bio/Biblio/Proceeding.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/alignment.pm $(INST_LIBDIR)/Bio/Biblio/Journal.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/segmented_keyglyph.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/transcript.pm $(INST_LIBDIR)/Bio/Cluster/SequenceFamily.pm $(INST_LIBDIR)/Bio/Tree/TreeFunctionsI.pm $(INST_LIBDIR)/Bio/LocationI.pm $(INST_LIBDIR)/Bio/Biblio/Provider.pm $(INST_LIBDIR)/Bio/Biblio/Person.pm $(INST_LIBDIR)/Bio/AlignIO/phylip.pm $(INST_LIBDIR)/Bio/DB/WebDBSeqI.pm $(INST_LIBDIR)/Bio/DB/Flat/BinarySearch.pm $(INST_LIBDIR)/Bio/Graphics.pm $(INST_LIBDIR)/Bio/Search/Hit/Fasta.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/ruler_arrow.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm $(INST_LIBDIR)/Bio/Ontology/RelationshipI.pm $(INST_LIBDIR)/Bio/Search/HSP/HSPFactory.pm $(INST_LIBDIR)/Bio/Root/Exception.pm $(INST_LIBDIR)/Bio/Ontology/OntologyStore.pm $(INST_LIBDIR)/Bio/Search/Processor.pm $(INST_LIBDIR)/Bio/Variation/Allele.pm $(INST_LIBDIR)/Bio/SeqFeature/FeaturePair.pm $(INST_LIBDIR)/Bio/Annotation/OntologyTerm.pm $(INST_LIBDIR)/Bio/Biblio/PubmedJournalArticle.pm $(INST_LIBDIR)/Bio/TreeIO/TreeEventBuilder.pm $(INST_LIBDIR)/Bio/SeqIO/embl.pm $(INST_LIBDIR)/Bio/WebAgent.pm $(INST_LIBDIR)/Bio/Biblio/IO/medline2ref.pm $(INST_LIBDIR)/Bio/SearchIO/FastHitEventBuilder.pm $(INST_LIBDIR)/Bio/Tree/NodeI.pm $(INST_LIBDIR)/Bio/Search/Hit/HitI.pm $(INST_LIBDIR)/Bio/Phenotype/MeSH/Twig.pm $(INST_LIBDIR)/Bio/Seq/PrimaryQual.pm $(INST_LIBDIR)/Bio/DB/NCBIHelper.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/xyplot.pm $(INST_LIBDIR)/Bio/Annotation/TypeManager.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Sopma.pm $(INST_LIBDIR)/Bio/Structure/StructureI.pm $(INST_LIBDIR)/Bio/SeqIO/largefasta.pm $(INST_LIBDIR)/Bio/Matrix/PSM/InstanceSite.pm $(INST_LIBDIR)/Bio/Tools/dpAlign.pm $(INST_LIBDIR)/Bio/Align/AlignI.pm $(INST_LIBDIR)/Bio/SeqFeature/PositionProxy.pm $(INST_LIBDIR)/Bio/Index/Abstract.pm $(INST_LIBDIR)/Bio/AlignIO.pm $(INST_LIBDIR)/Bio/Factory/SeqAnalysisParserFactory.pm $(INST_LIBDIR)/Bio/Biblio.pm $(INST_LIBDIR)/Bio/Restriction/Analysis.pm $(INST_LIBDIR)/Bio/Matrix/PSM/IO.pm $(INST_LIBDIR)/Bio/Seq/SeqFastaSpeedFactory.pm $(INST_LIBDIR)/Bio/Factory/SequenceFactoryI.pm $(INST_LIBDIR)/Bio/Structure/Residue.pm $(INST_LIBDIR)/Bio/SeqIO/fasta.pm $(INST_LIBDIR)/Bio/PopGen/IO/prettybase.pm $(INST_LIBDIR)/Bio/AlignIO/maf.pm $(INST_LIBDIR)/Bio/Restriction/Enzyme/MultiSite.pm $(INST_LIBDIR)/Bio/Search/Result/HMMERResult.pm $(INST_LIBDIR)/Bio/Tools/FootPrinter.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/GOR4.pm $(INST_LIBDIR)/Bio/Search/Result/BlastResult.pm $(INST_LIBDIR)/Bio/MapIO/mapmaker.pm $(INST_LIBDIR)/Bio/Tools/Blast.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/dot.pm $(INST_LIBDIR)/Bio/Seq/Meta/Array.pm $(INST_LIBDIR)/bioperl.pod $(INST_LIBDIR)/Bio/Structure/IO/pdb.pm $(INST_LIBDIR)/Bio/Map/LinkageMap.pm $(INST_LIBDIR)/Bio/DB/SwissProt.pm $(INST_LIBDIR)/Bio/Matrix/PSM/IO/transfac.pm $(INST_LIBDIR)/Bio/Tools/Signalp.pm $(INST_LIBDIR)/Bio/Phenotype/Measure.pm $(INST_LIBDIR)/Bio/Factory/ApplicationFactoryI.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/TranscriptI.pm $(INST_LIBDIR)/Bio/LiveSeq/Range.pm $(INST_LIBDIR)/Bio/Coordinate/Utils.pm $(INST_LIBDIR)/Bio/Search/Result/WABAResult.pm $(INST_LIBDIR)/Bio/DB/RandomAccessI.pm $(INST_LIBDIR)/Bio/PopGen/Simulation/GeneticDrift.pm $(INST_LIBDIR)/Bio/DB/GFF/Feature.pm $(INST_LIBDIR)/Bio/Tools/Blast/CHANGES $(INST_LIBDIR)/Bio/DB/Biblio/soap.pm $(INST_LIBDIR)/Bio/DB/Failover.pm $(INST_LIBDIR)/Bio/Tools/HMMER/Results.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm $(INST_LIBDIR)/Bio/Variation/RNAChange.pm $(INST_LIBDIR)/Bio/Tools/Run/README $(INST_LIBDIR)/Bio/TreeIO/lintree.pm $(INST_LIBDIR)/Bio/Graphics/Pictogram.pm $(INST_LIBDIR)/Bio/Factory/AnalysisI.pm $(INST_LIBDIR)/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/dna.pm $(INST_LIBDIR)/Bio/Phenotype/OMIM/OMIMparser.pm $(INST_LIBDIR)/Bio/SeqFeature/SiRNA/Pair.pm $(INST_LIBDIR)/Bio/SeqFeature/Similarity.pm $(INST_LIBDIR)/Bio/Location/CoordinatePolicyI.pm $(INST_LIBDIR)/Bio/Expression/FeatureI.pm $(INST_LIBDIR)/Bio/SeqIO/fastq.pm $(INST_LIBDIR)/Bio/Tools/Genscan.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/generic.pm $(INST_LIBDIR)/Bio/Map/SimpleMap.pm $(INST_LIBDIR)/Bio/Search/Hit/PsiBlastHit.pm $(INST_LIBDIR)/Bio/Search/HSP/WABAHSP.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/ResultTableWriter.pm $(INST_LIBDIR)/Bio/AlignIO/fasta.pm $(INST_LIBDIR)/Bio/Map/Marker.pm $(INST_LIBDIR)/Bio/Factory/SequenceStreamI.pm $(INST_LIBDIR)/Bio/AlignIO/clustalw.pm $(INST_LIBDIR)/Bio/Coordinate/MapperI.pm $(INST_LIBDIR)/Bio/DB/Fasta.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/dbi/iterator.pm $(INST_LIBDIR)/Bio/Phenotype/OMIM/OMIMentry.pm $(INST_LIBDIR)/Bio/Seq/QualI.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Scansite.pm $(INST_LIBDIR)/Bio/Tools/HMMER/Domain.pm $(INST_LIBDIR)/Bio/Graphics/FeatureFile/Iterator.pm $(INST_LIBDIR)/Bio/Das/FeatureTypeI.pm $(INST_LIBDIR)/Bio/DB/GDB.pm $(INST_LIBDIR)/Bio/Cluster/UniGeneI.pm $(INST_LIBDIR)/Bio/Biblio/JournalArticle.pm $(INST_LIBDIR)/Bio/Tools/Blast/Sbjct.pm $(INST_LIBDIR)/Bio/Index/EMBL.pm $(INST_LIBDIR)/Bio/Das/SegmentI.pm $(INST_LIBDIR)/Bio/Search/Hit/GenericHit.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_acembly.pm $(INST_LIBDIR)/Bio/Ontology/OntologyI.pm $(INST_LIBDIR)/Bio/DB/GFF/Segment.pm $(INST_LIBDIR)/Bio/SeqIO/gcg.pm $(INST_LIBDIR)/Bio/Tools/Lucy.pm $(INST_LIBDIR)/Bio/Biblio/WebResource.pm $(INST_LIBDIR)/Bio/TreeIO/svggraph.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_softberry.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/Poly_A_site.pm $(INST_LIBDIR)/Bio/RangeI.pm $(INST_LIBDIR)/Bio/Symbol/DNAAlphabet.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/ELM.pm $(INST_LIBDIR)/Bio/PrimarySeq.pm $(INST_LIBDIR)/Bio/Biblio/TechReport.pm $(INST_LIBDIR)/Bio/Seq/EncodedSeq.pm $(INST_LIBDIR)/Bio/PopGen/IndividualI.pm $(INST_LIBDIR)/Bio/Factory/MapFactoryI.pm $(INST_LIBDIR)/Bio/Ontology/RelationshipFactory.pm $(INST_LIBDIR)/Bio/Tree/NodeNHX.pm $(INST_LIBDIR)/Bio/SearchIO.pm $(INST_LIBDIR)/Bio/LiveSeq/SeqI.pm $(INST_LIBDIR)/Bio/Tools/Genemark.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/extending_arrow.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/coding.pm $(INST_LIBDIR)/Bio/SearchIO/exonerate.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/segments.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/none.pm $(INST_LIBDIR)/Bio/SeqFeature/SimilarityPair.pm $(INST_LIBDIR)/Bio/Ontology/RelationshipType.pm $(INST_LIBDIR)/Bio/Structure/SecStr/DSSP/Res.pm $(INST_LIBDIR)/Bio/PopGen/Population.pm $(INST_LIBDIR)/Bio/PopGen/Simulation/Coalescent.pm $(INST_LIBDIR)/Bio/PopGen/Statistics.pm $(INST_LIBDIR)/Bio/DB/GFF/Adaptor/biofetch_oracle.pm $(INST_LIBDIR)/Bio/Structure/Model.pm $(INST_LIBDIR)/Bio/Search/HSP/HSPI.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm $(INST_LIBDIR)/Bio/Index/AbstractSeq.pm $(INST_LIBDIR)/Bio/Seq/RichSeq.pm $(INST_LIBDIR)/Bio/Expression/FeatureSet/FeatureSetMas50.pm $(INST_LIBDIR)/Bio/Tree/AlleleNode.pm $(INST_LIBDIR)/Bio/DB/RefSeq.pm $(INST_LIBDIR)/bioscripts.pod $(INST_LIBDIR)/Bio/DB/InMemoryCache.pm $(INST_LIBDIR)/Bio/ClusterIO.pm $(INST_LIBDIR)/Bio/TreeIO/nexus.pm $(INST_LIBDIR)/Bio/Graphics/Panel.pm $(INST_LIBDIR)/Bio/Cluster/FamilyI.pm $(INST_LIBDIR)/Bio/LiveSeq/Prim_Transcript.pm $(INST_LIBDIR)/Bio/SeqIO/game/gameSubs.pm $(INST_LIBDIR)/Bio/Tools/Run/StandAloneBlast.pm $(INST_LIBDIR)/Bio/Symbol/Symbol.pm $(INST_LIBDIR)/Bio/Biblio/IO.pm $(INST_LIBDIR)/Bio/Factory/DriverFactory.pm $(INST_LIBDIR)/Bio/PopGen/IO/csv.pm $(INST_LIBDIR)/Bio/Tree/Tree.pm $(INST_LIBDIR)/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Domcut.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/primers.pm $(INST_LIBDIR)/Bio/Tools/Analysis/Protein/Mitoprot.pm $(INST_LIBDIR)/Bio/SeqIO/game/gameWriter.pm $(INST_LIBDIR)/Bio/Tools/Prediction/Exon.pm $(INST_LIBDIR)/Bio/SearchIO/wise.pm $(INST_LIBDIR)/Bio/Phenotype/OMIM/MiniMIMentry.pm $(INST_LIBDIR)/Bio/SimpleAnalysisI.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/crossbox.pm $(INST_LIBDIR)/Bio/Tools/Blast/HSP.pm $(INST_LIBDIR)/Bio/Seq/Meta.pm $(INST_LIBDIR)/Bio/SeqFeature/AnnotationAdaptor.pm $(INST_LIBDIR)/Bio/Tools/SeqStats.pm $(INST_LIBDIR)/Bio/LiveSeq/ChainI.pm $(INST_LIBDIR)/Bio/Variation/SeqDiff.pm $(INST_LIBDIR)/Bio/SeqFeature/SiRNA/Oligo.pm $(INST_LIBDIR)/Bio/Search/Hit/BlastHit.pm $(INST_LIBDIR)/Bio/Assembly/Scaffold.pm $(INST_LIBDIR)/Bio/Tools/Primer3.pm $(INST_LIBDIR)/Bio/Matrix/Generic.pm $(INST_LIBDIR)/Bio/SearchIO/blastxml.pm $(INST_LIBDIR)/Bio/UpdateableSeqI.pm $(INST_LIBDIR)/Bio/Restriction/IO.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/Exon.pm $(INST_LIBDIR)/Bio/Map/MarkerI.pm $(INST_LIBDIR)/Bio/Matrix/IO/phylip.pm $(INST_LIBDIR)/Bio/DB/BiblioI.pm $(INST_LIBDIR)/Bio/SearchIO/waba.pm $(INST_LIBDIR)/Bio/Species.pm $(INST_LIBDIR)/Bio/Tools/pSW.pm $(INST_LIBDIR)/Bio/Coordinate/Pair.pm $(INST_LIBDIR)/Bio/IdentifiableI.pm $(INST_LIBDIR)/Bio/LiveSeq/IO/README $(INST_LIBDIR)/Bio/Index/GenBank.pm $(INST_LIBDIR)/Bio/AlignIO/stockholm.pm $(INST_LIBDIR)/Bio/LiveSeq/IO/BioPerl.pm $(INST_LIBDIR)/Bio/Ontology/GOterm.pm $(INST_LIBDIR)/Bio/Tools/Seg.pm $(INST_LIBDIR)/Bio/Tools/AlignFactory.pm $(INST_LIBDIR)/Bio/DB/Taxonomy/entrez.pm $(INST_LIBDIR)/Bio/SearchIO/sim4.pm $(INST_LIBDIR)/Bio/OntologyIO/simplehierarchy.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/Intron.pm $(INST_LIBDIR)/Bio/Search/HSP/BlastHSP.pm $(INST_LIBDIR)/Bio/DB/Flat/BDB/swiss.pm $(INST_LIBDIR)/Bio/Tools/Promoterwise.pm $(INST_LIBDIR)/Bio/Map/MapI.pm $(INST_LIBDIR)/Bio/Tools/Phylo/PAML/ModelResult.pm $(INST_LIBDIR)/Bio/Location/Atomic.pm $(INST_LIBDIR)/Bio/Root/Utilities.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/pinsertion.pm $(INST_LIBDIR)/Bio/SeqIO/genbank.pm $(INST_LIBDIR)/Bio/PopGen/IO.pm $(INST_LIBDIR)/Bio/Matrix/IO/scoring.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/arrow.pm $(INST_LIBDIR)/Bio/Biblio/Service.pm $(INST_LIBDIR)/Bio/Map/Microsatellite.pm $(INST_LIBDIR)/Bio/Tools/Primer/Pair.pm $(INST_LIBDIR)/Bio/DB/GFF/Featname.pm $(INST_LIBDIR)/Bio/SearchIO/Writer/HitTableWriter.pm $(INST_LIBDIR)/Bio/Tools/EPCR.pm $(INST_LIBDIR)/Bio/Graphics/Glyph/line.pm $(INST_LIBDIR)/Bio/SeqFeature/Gene/ExonI.pm $(INST_LIBDIR)/Bio/DB/Flat.pm $(INST_LIBDIR)/Bio/Assembly/IO/phrap.pm $(INST_LIBDIR)/Bio/Taxonomy/Tree.pm $(INST_LIBDIR)/Bio/Location/Fuzzy.pm $(INST_LIBDIR)/Bio/Index/Blast.pm $(INST_LIBDIR)/Bio/SeqFeature/Collection.pm $(INST_LIBDIR)/Bio/Tools/Analysis/DNA/ESEfinder.pm $(INST_LIBDIR)/Bio/TreeIO/newick.pm $(INST_LIBDIR)/Bio/SeqIO/MultiFile.pm $(INST_LIBDIR)/Bio/Tools/RestrictionEnzyme.pm $(INST_LIBDIR)/Bio/Tools/Primer/Assessor/Base.pm $(INST_LIBDIR)/Bio/Search/HSP/FastaHSP.pm $(INST_LIBDIR)/Bio/Map/PositionI.pm $(INST_LIBDIR)/Bio/Coordinate/Result.pm $(INST_LIBDIR)/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm $(INST_LIBDIR)/Bio/DB/Query/WebQuery.pm $(INST_LIBDIR)/Bio/Seq/SeqFactory.pm $(INST_LIBDIR)/Bio/Root/Storable.pm $(INST_LIBDIR)/Bio/SearchIO/fasta.pm $(INST_LIBDIR)/Bio/Root/Root.pm $(INST_LIBDIR)/Bio/Phenotype/Correlate.pm $(INST_LIBDIR)/Bio/Tools/pICalculator.pm $(INST_LIBDIR)/Bio/Matrix/PSM/PsmI.pm $(INST_LIBDIR)/Bio/LiveSeq/Exon.pm $(INST_LIBDIR)/Bio/PopGen/MarkerI.pm
rm -rf Makefile Makefile.old ./Seq.pm.bak
# --- MakeMaker dist_basics section:
distclean :: realclean distcheck
distcheck :
$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Manifest=fullcheck \
-e fullcheck
skipcheck :
$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Manifest=skipcheck \
-e skipcheck
manifest :
$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Manifest=mkmanifest \
-e mkmanifest
# --- MakeMaker dist_core section:
dist : $(DIST_DEFAULT)
@$(PERL) -le 'print "Warning: Makefile possibly out of date with $$vf" if ' \
-e '-e ($$vf="$(VERSION_FROM)") and -M $$vf < -M "Makefile";'
tardist : $(DISTVNAME).tar$(SUFFIX)
zipdist : $(DISTVNAME).zip
$(DISTVNAME).tar$(SUFFIX) : distdir
$(PREOP)
$(TO_UNIX)
$(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME)
$(RM_RF) $(DISTVNAME)
$(COMPRESS) $(DISTVNAME).tar
$(POSTOP)
$(DISTVNAME).zip : distdir
$(PREOP)
$(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME)
$(RM_RF) $(DISTVNAME)
$(POSTOP)
uutardist : $(DISTVNAME).tar$(SUFFIX)
uuencode $(DISTVNAME).tar$(SUFFIX) \
$(DISTVNAME).tar$(SUFFIX) > \
$(DISTVNAME).tar$(SUFFIX)_uu
shdist : distdir
$(PREOP)
$(SHAR) $(DISTVNAME) > $(DISTVNAME).shar
$(RM_RF) $(DISTVNAME)
$(POSTOP)
# --- MakeMaker dist_dir section:
distdir :
$(RM_RF) $(DISTVNAME)
$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Manifest=manicopy,maniread \
-e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');"
# --- MakeMaker dist_test section:
disttest : distdir
cd $(DISTVNAME) && $(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) Makefile.PL
cd $(DISTVNAME) && $(MAKE)
cd $(DISTVNAME) && $(MAKE) test
# --- MakeMaker dist_ci section:
ci :
$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::Manifest=maniread \
-e "@all = keys %{ maniread() };" \
-e 'print("Executing $(CI) @all\n"); system("$(CI) @all");' \
-e 'print("Executing $(RCS_LABEL) ...\n"); system("$(RCS_LABEL) @all");'
# --- MakeMaker install section:
install :: all pure_install doc_install
install_perl :: all pure_perl_install doc_perl_install
install_site :: all pure_site_install doc_site_install
install_ :: install_site
@echo INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
pure_install :: pure_$(INSTALLDIRS)_install
doc_install :: doc_$(INSTALLDIRS)_install
@echo Appending installation info to $(INSTALLARCHLIB)/perllocal.pod
pure__install : pure_site_install
@echo INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
doc__install : doc_site_install
@echo INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
pure_perl_install ::
@$(MOD_INSTALL) \
read $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist \
write $(INSTALLARCHLIB)/auto/$(FULLEXT)/.packlist \
$(INST_LIB) $(INSTALLPRIVLIB) \
$(INST_ARCHLIB) $(INSTALLARCHLIB) \
$(INST_BIN) $(INSTALLBIN) \
$(INST_SCRIPT) $(INSTALLSCRIPT) \
$(INST_HTMLLIBDIR) $(INSTALLHTMLPRIVLIBDIR) \
$(INST_HTMLSCRIPTDIR) $(INSTALLHTMLSCRIPTDIR) \
$(INST_MAN1DIR) $(INSTALLMAN1DIR) \
$(INST_MAN3DIR) $(INSTALLMAN3DIR)
@$(WARN_IF_OLD_PACKLIST) \
$(SITEARCHEXP)/auto/$(FULLEXT)
pure_site_install ::
@$(MOD_INSTALL) \
read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \
write $(INSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \
$(INST_LIB) $(INSTALLSITELIB) \
$(INST_ARCHLIB) $(INSTALLSITEARCH) \
$(INST_BIN) $(INSTALLBIN) \
$(INST_SCRIPT) $(INSTALLSCRIPT) \
$(INST_HTMLLIBDIR) $(INSTALLHTMLSITELIBDIR) \
$(INST_HTMLSCRIPTDIR) $(INSTALLHTMLSCRIPTDIR) \
$(INST_MAN1DIR) $(INSTALLMAN1DIR) \
$(INST_MAN3DIR) $(INSTALLMAN3DIR)
@$(WARN_IF_OLD_PACKLIST) \
$(PERL_ARCHLIB)/auto/$(FULLEXT)
doc_perl_install ::
-@$(MKPATH) $(INSTALLARCHLIB)
-@$(DOC_INSTALL) \
"Module" "$(NAME)" \
"installed into" "$(INSTALLPRIVLIB)" \
LINKTYPE "$(LINKTYPE)" \
VERSION "$(VERSION)" \
EXE_FILES "$(EXE_FILES)" \
>> $(INSTALLARCHLIB)/perllocal.pod
doc_site_install ::
-@$(MKPATH) $(INSTALLARCHLIB)
-@$(DOC_INSTALL) \
"Module" "$(NAME)" \
"installed into" "$(INSTALLSITELIB)" \
LINKTYPE "$(LINKTYPE)" \
VERSION "$(VERSION)" \
EXE_FILES "$(EXE_FILES)" \
>> $(INSTALLARCHLIB)/perllocal.pod
uninstall :: uninstall_from_$(INSTALLDIRS)dirs
uninstall_from_perldirs ::
@$(UNINSTALL) $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist
uninstall_from_sitedirs ::
@$(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist
# --- MakeMaker force section:
# Phony target to force checking subdirectories.
FORCE:
@$(NOOP)
# --- MakeMaker perldepend section:
# --- MakeMaker makefile section:
# We take a very conservative approach here, but it\'s worth it.
# We move Makefile to Makefile.old here to avoid gnu make looping.
Makefile : Makefile.PL $(CONFIGDEP)
@echo "Makefile out-of-date with respect to $?"
@echo "Cleaning current config before rebuilding Makefile..."
-@$(RM_F) Makefile.old
-@$(MV) Makefile Makefile.old
-$(MAKE) -f Makefile.old clean $(DEV_NULL) || $(NOOP)
$(PERL) "-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" Makefile.PL
@echo "==> Your Makefile has been rebuilt. <=="
@echo "==> Please rerun the make command. <=="
false
# To change behavior to :: would be nice, but would break Tk b9.02
# so you find such a warning below the dist target.
#Makefile :: $(VERSION_FROM)
# @echo "Warning: Makefile possibly out of date with $(VERSION_FROM)"
# --- MakeMaker staticmake section:
# --- MakeMaker makeaperl section ---
MAP_TARGET = perl
FULLPERL = /usr/bin/perl
$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
$(MAKE) -f $(MAKE_APERL_FILE) $@
$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE)
@echo Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
@$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) \
Makefile.PL DIR= \
MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
MAKEAPERL=1 NORECURS=1 CCCDLFLAGS=
# --- MakeMaker test section:
TEST_VERBOSE=0
TEST_TYPE=test_$(LINKTYPE)
TEST_FILE = test.pl
TEST_FILES =
TESTDB_SW = -d
testdb :: testdb_$(LINKTYPE)
test :: $(TEST_TYPE)
@echo 'No tests defined for $(NAME) extension.'
test_dynamic :: pure_all
testdb_dynamic :: pure_all
PERL_DL_NONLAZY=1 $(FULLPERL) $(TESTDB_SW) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) $(TEST_FILE)
test_ : test_dynamic
test_static :: test_dynamic
testdb_static :: testdb_dynamic
# --- MakeMaker ppd section:
# Creates a PPD (Perl Package Description) for a binary distribution.
ppd:
@$(PERL) -e "print qq{<SOFTPKG NAME=\"bioperl\" VERSION=\"1,4,0,0\">\n}. qq{\t<TITLE>bioperl</TITLE>\n}. qq{\t<ABSTRACT>Bioinformatics Toolkit</ABSTRACT>\n}. qq{\t<AUTHOR>Bioperl Team (bioperl-l\@bioperl.org)</AUTHOR>\n}. qq{\t<IMPLEMENTATION>\n}. qq{\t\t<DEPENDENCY NAME=\"DB_File\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"File-Spec\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"File-Temp\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"HTML-Entities\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"IO-Scalar\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<DEPENDENCY NAME=\"IO-String\" VERSION=\"0,0,0,0\" />\n}. qq{\t\t<OS NAME=\"$(OSNAME)\" />\n}. qq{\t\t<ARCHITECTURE NAME=\"alpha-dec_osf\" />\n}. qq{\t\t<CODEBASE HREF=\"\" />\n}. qq{\t</IMPLEMENTATION>\n}. qq{</SOFTPKG>\n}" > bioperl.ppd
# --- MakeMaker pm_to_blib section:
pm_to_blib: $(TO_INST_PM)
@$(PERL) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" \
"-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" -MExtUtils::Install \
-e "pm_to_blib({qw{$(PM_TO_BLIB)}},'$(INST_LIB)/auto')"
@$(TOUCH) $@
# --- MakeMaker selfdocument section:
# --- MakeMaker postamble section:
show_tests :
@echo 'type make test_<subtest> to run'
@echo ''
# End.
-------------- next part --------------
-------------------------------
Dr. Wolf-Gerolf THIES
ITG - Tox, Bau 439, Zi 507
Forschungszentrum Karlsruhe
Postfach 3640
D-76021 Karlsruhe
Tel: +49 7247 82-3139/-3547
Fax: +49 7247 82 3557
E-mail: thies at itg.fzk.de
--------------------------------
More information about the Bioperl-l
mailing list