[Bioperl-announce-l] bioperl-1.5.0 released

Jason Stajich jason.stajich at duke.edu
Mon Jan 24 21:36:39 EST 2005

Bioperl 1.5.0 Developer's release is available for download.


We'll update the website to reflect this new release.

The odd-numbered releases are called developer releases and are not 
deposited on CPAN.  Please note that the API in 1.5.0 may change before 
the 1.6.0 release. which will be consider a stable API.  We may do 
another developer release before 1.6.0 goes out.

Lots of people have contributed to this release, I apologize for not 
naming them all.  I'll try to cover some: thanks to Aaron Mackey for 
getting this release started, Brian Osborne for extensive documentation 
improvements, Nathan Haigh for volunteering to make a PPM of the 
release and Barry Moore and Nathan answering many of the windows 
related questions, Allen Day & Scott Cain & Steffen Grossmann for the 
work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for 
the work with Unflattener to merge GenBank annotations into GFF3 

Please see the AUTHORS file for a complete list of contributors.

Jason Stajich on behalf of the Bioperl developers.

Here is the info from the Changes file.
1.5 Developer release

     o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
       provide Jukes-Cantor and Kimura pairwise distance methods,

     o Bio::AlignIO support for "po" format of POA, and "maf";
       Bio::AlignIO::largemultifasta is a new alternative to
       Bio::AlignIO::fasta for temporary file-based manipulation of
       particularly large multiple sequence alignments.

     o Bio::Assembly::Singlet allows orphan, unassembled sequences to
       be treated similarly as an assembled contig.

     o Bio::CodonUsage provides new rare_codon() and probable_codons()
       methods for identifying particular codons that encode a given
       amino acid.

     o Bio::Coordinate::Utils provides new from_align() method to build
       a Bio::Coordinate pair directly from a
       Bio::Align::AlignI-conforming object.

     o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
       Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
       web service using standard Pubmed query syntax, and retrieve
       results as XML.

     o Bio::DB::GFF has various sundry bug fixes.

     o Bio::FeatureIO is a new SeqIO-style subsystem for
       writing/reading genomic features to/from files.  I/O classes
       exist for BED, GTF (aka GFF v2.5), and GFF v3.  Bio::FeatureIO
       classes only read/write Bio::SeqFeature::Annotated objects.
       Notably, the GFF v3 class requires features to be typed into the
       Sequence Ontology.

     o Bio::Graph namespace contains new modules for manipulation and
       analysis of protein interaction graphs.

     o Bio::Graphics has many bug fixes and shiny new glyphs.

     o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
       indexing for HMMER reports and FASTA qual files, respectively.

     o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
       new objects that can be placed within a Bio::Map::MapI-compliant
       genetic/physical map; Bio::Map::Physical provides a new physical
       map type; Bio::MapIO::fpc provides finger-printed clone mapping

     o Bio::Matrix::PSM provide new support for postion-specific
       (scoring) matrices (e.g. profiles, or "possums").

     o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
       be instantiated without explicitly using Bio::OntologyIO.  This
       is possible through changes to Bio::Ontology::OntologyStore to
       download ontology files from the web as necessary.  Locations of
       ontology files are hard-coded into

     o Bio::PopGen includes many new methods and data types for
       population genetics analyses.

     o New constructor to Bio::Range, unions().  Given a list of
       ranges, returns another list of "flattened" ranges --
       overlapping ranges are merged into a single range with the
       mininum and maximum coordinates of the entire overlapping group.

     o Bio::Root::IO now supports -url, in addition to -file and -fh.
       The new -url argument allows one to specify the network address
       of a file for input.  -url currently only works for GET
       requests, and thus is read-only.

     o Bio::SearchIO::hmmer now returns individual Hit objects for each
       domain alignment (thus containing only one HSP); previously
       separate alignments would be merged into one hit if the domain
       involved in the alignments was the same, but this only worked
       when the repeated domain occured without interruption by any
       other domain, leading to a confusing mixture of Hit and HSP

     o Bio::Search::Result::ResultI-compliant report objects now
       implement the "get_statistics" method to access
       Bio::Search::StatisticsI objects that encapsulate any
       statistical parameters associated with the search (e.g. Karlin's
       lambda for BLAST/FASTA).

     o Bio::Seq::LargeLocatableSeq combines the functionality already
       found in Bio::Seq::LargeSeq and Bio::LocatableSeq.

     o Bio::SeqFeature::Annotated is a replacement for
       Bio::SeqFeature::Generic.  It breaks compliance with the
       Bio::SeqFeatureI interface because the author was sick of
       dealing with untyped annotation tags.  All
       Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
       compliant, and accessible through Bio::Annotation::Collection.

     o Bio::SeqFeature::Primer implements a Tm() method for primer
       melting point predictions.

     o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
       InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.

     o Bio::Taxonomy::Node now implements the methods necessary for
       Bio::Species interoperability.

     o Bio::Tools::CodonTable has new reverse_translate_all() and
       make_iupac_string() methods.

     o Bio::Tools::dpAlign now provides sequence profile alignments.

     o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).

     o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report

     o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
       for designing small inhibitory RNA.

     o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
       methods based on a distance matrix.

     o Bio::Tree::Statistics provides an assess_bootstrap() method to
       calculate bootstrap support values on a guide tree topology,
       based on provided bootstrap tree topologies.

     o Bio::TreeIO now supports the Pagel (PAG) tree format.

Jason Stajich
jason.stajich at duke.edu
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