Proposal: new menu layout, with examples

[Gary Williams, Tel 01223 494522]

Attached is my attempt at allocating programs to the menu structure.

Most things fit well and there are only a few programs with assignments
to multiple groups:
23 to two groups, 2 to three groups (remap and showseq)

It there are no complaints, I'll start changing the ACD files soon (next
week?)

Gary
-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK
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+Alignment
+    Consensus    (merging sequences to make a consensus)
=	cons
=	megamerger
=	merger
+    Differences
=	diffseq
+    Dot plots
=	dotmatcher
=	dotpath
=	dottup
=	polydot
+    Global
=	est2genome
=	needle
=	stretcher
+    Local
=	matcher
=	seqmatchall
=	water
=	wordmatch
+    Multiple
=	emma
=	mse
=	plotcon
=	prettyplot
+Display        (publication display, not just stuff that plots results)
=	abiview
=	cirdna
=	lindna
=	prettyplot
=	prettyseq
=	remap
=	showdb
=	showseq
=	pepnet
=	pepwheel
=	seealso
=	showfeat
=	showseq
+Edit            (sequence and annotation manipulation)
=	cutseq
=	degapseq
=	descseq
=	entret
=	extractseq
=	infoseq
=	maskfeat
=	mse
=	newseq
=	noreturn
=	notseq
=	nthseq
=	pasteseq
=	revseq
=	seqret
=	seqretall
=	seqretset
=	seqretsplit
=	splitter
=	textsearch
=	trimseq
=	vectorstrip
+Enzyme Kinetics
=	findkm
+Feature tables        (manipulation and display of feature tables)
=	coderet
=	showfeat
+Help            (help for the user)
=	infoseq
=	seealso
=	showdb
=	tfm
=	wossname
+Nucleic
+    2D Structure    (RNA structure)
+    Codon usage
=	cai
=	chips
=	codcmp
=	cusp
=	syco
+    Composition    (properties over the whole sequence, GFF not produced)
=	banana
=	btwisted
=	chaos
=	compseq
=	dan
=	freak
=	isochore
=	wordcount
+    CPG islands
=	cpgplot
=	cpgreport
=	geecee
=	newcpgreport
=	newcpgseek
+    Gene finding    (genes and other genomic features)
=	est2genome
=	getorf
=	marscan
=	plotorf
=	showorf
=	wobble
+    Motifs        (search for defined patterns)
=	dreg
=	fuzznuc
=	fuzztran
=	marscan
+    Mutation
=	msbar
=	shuffleseq
+    Primers  
=	prima
=	primersearch
=	stssearch
+    Profiles    (search for defined profiles)
=	profit
=	prophecy
=	prophet
+    Repeats
=	einverted
=	equicktandem
=	etandem
=	palindrome
+    Restriction
=	recode
=	redata
=	remap
=	restover
=	restrict
=	showseq
=	silent
+    Transcription    (transcription factors)
=	tfscan
+    Translation
=	backtranseq
=	coderet
=	prettyseq
=	plotorf
=	remap
=	showorf
=	showseq
=	transeq
+    Mutation
+Phylogeny        (mainly the Phylip package)
=	distmat
+Protein
+    2D Structure    (2D structure and topological features)
=	garnier
=	helixturnhelix
=	hmoment
=	tmap
=	pepcoil
=	pepnet
=	pepwheel
+    3D Structure
+    Composition    (properties over the whole sequence, GFF not produced)
=	backtranseq
=	charge
=	checktrans
=	compseq
=	emowse
=	iep
=	octanol
=	pepinfo
=	pepstats
=	pepwindow
=	pepwindowall
+    Motifs        (search for defined patterns)
=	antigenic
=	digest
=	fuzzpro
=	fuzztran
=	helixturnhelix
=	oddcomp
=	patmatdb
=	patmatmotifs
=	pepcoil
=	preg
=	pscan
=	sigcleave
+    Mutation
=	msbar
=	shuffleseq
+    Profiles    (search for defined profiles)
=	profit
=	prophecy
=	prophet
+Utils
+    Database indexing
=	dbiblast
=	dbifasta
=	dbiflat
=	dbigcg
+    Database creation
=	domainer
=	nrscope
=	printsextract
=	prosextract
=	rebaseextract
=	scope
=	tfextract
+    Misc        
=	embossdata
+Test
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abiview		Display
antigenic	Protein:Motifs
backtranseq	Nucleic:Translation, Protein:Composition
banana		Nucleic:Composition
btwisted	Nucleic:Composition
cai		Nucleic:Codon usage
chaos		Nucleic:Composition
charge		Protein:Composition
checktrans	Protein:Composition
chips		Nucleic:Codon usage
cirdna		Display
codcmp		Nucleic:Codon usage
coderet		Feature tables, Nucleic:Translation
compseq		Nucleic:Composition, Protein:Composition
cons		Alignment:Consensus
cpgplot		Nucleic:CpG Islands
cpgreport	Nucleic:CpG Islands
cusp		Nucleic:Codon usage
cutseq		Edit
dan		Nucleic:Composition
dbiblast	Utils:Database indexing
dbifasta	Utils:Database indexing
dbiflat		Utils:Database indexing
dbigcg		Utils:Database indexing
degapseq	Edit
descseq		Edit
diffseq		Alignment:Differences
digest		Protein:Motifs
distmat		Phylogeny
domainer	Utils:Database creation
dotmatcher	Alignment:Dot plots
dotpath		Alignment:Dot plots
dottup		Alignment:Dot plots
dreg		Nucleic:Motifs
einverted	Nucleic:Repeats
embossdata	Utils:Misc
emowse		Protein:Composition
equicktandem	Nucleic:Repeats
etandem		Nucleic:Repeats
emma		Alignment:Multiple
entret		Edit
est2genome	Alignment:Global
extractseq	Edit
freak		Nucleic:Composition
fuzznuc		Nucleic:Motifs
fuzzpro		Protein:Motifs
fuzztran	Nucleic:Motifs, Protein:Motifs
garnier		Protein:2D Structure
geecee		Nucleic:CpG Islands
getorf		Nucleic:Gene finding
helixturnhelix	Protein:2D Structure, Protein:Motifs
hmoment		Protein:2D Structure
iep		Protein:Composition
infoseq		Edit, Help
isochore	Nucleic:Composition
lindna		Display
marscan		Nucleic:Gene finding, Nucleic:Motifs
maskfeat	Edit
matcher		Alignment:Local
megamerger	Alignment:Consensus
merger		Alignment:Consensus
msbar		Nucleic:Mutation, Protein:Mutation
mse		Alignment:Multiple, Edit
needle		Alignment:Global
newcpgreport	Nucleic:CpG Islands 
newcpgseek	Nucleic:CpG Islands 
newseq		Edit
noreturn	Edit
notseq		Edit
nthseq		Edit
nrscope		Utils:Database creation
octanol		Protein:Composition
oddcomp		Protein:Motifs
palindrome	Nucleic:Repeats
pasteseq	Edit
patmatdb	Protein:Motifs
patmatmotifs	Protein:Motifs
pepcoil		Protein:2D Structure, Protein:Motifs
pepinfo		Protein:Composition
pepnet		Display, Protein:2D Structure
pepstats	Protein:Composition
pepwheel	Display, Protein:2D Structure
pepwindow	Protein:Composition
pepwindowall	Protein:Composition
plotcon		Alignment:Multiple
plotorf		Nucleic:Gene finding, Nucleic:Translation
polydot		Alignment:Dot plots
preg		Protein:Motifs
prettyplot	Alignment:Multiple, Display
prettyseq	Display, Nucleic:Translation
prima		Nucleic:Primers
primersearch	Nucleic:Primers
printsextract	Utils:Database creation
profit		Nucleic:Profiles, Protein:Profiles
prophecy	Nucleic:Profiles, Protein:Profiles
prophet		Nucleic:Profiles, Protein:Profiles
prosextract	Utils:Database creation
pscan		Protein:Motifs
rebaseextract	Utils:Database creation
recode		Nucleic:Restriction
redata		Nucleic:Restriction
remap		Display, Nucleic:Restriction, Nucleic:Translation
restover	Nucleic:Restriction
restrict	Nucleic:Restriction
revseq		Edit
scope		Utils:Database creation
seealso		Display, Help
seqmatchall	Alignment:Local
seqret		Edit
seqretall	Edit
seqretset	Edit
seqretsplit	Edit
showdb		Display, Help
showfeat	Display, Feature tables
showorf		Nucleic:Gene finding, Nucleic:Translation
showseq		Display, Nucleic:Translation, Nucleic:Restriction
shuffleseq	Nucleic:Mutation, Protein:Mutation
sigcleave	Protein:Motifs
silent		Nucleic:Restriction
stretcher	Alignment:Global
stssearch	Nucleic:Primers
splitter	Edit
supermatcher	Alignment:Local
syco		Nucleic:Codon usage
tfextract	Utils:Database creation
tfm		Help
tfscan		Nucleic:Transcription
transeq		Nucleic:Translation
trimseq		Edit
textsearch	Edit
tmap		Protein:2D Structure
vectorstrip	Edit
wobble		Nucleic:Gene finding
wordcount	Nucleic:Composition
wordmatch	Alignment:Local
water		Alignment:Local
wossname	Help