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Acd
acdvalid
acdtrace
acdtable
acdpretty
acdlog
acdc
Alignment
FastTree
dialign
Alignment > Consensus
cons
consambig
gap4
megamerger
merger
spin
Alignment > Differences
act
diffseq
Alignment > Dot_plots
dotmatcher
dotpath
dotter
dottup
polydot
Alignment > Editing
clcsequenceviewer
jalview
squint
Alignment > Global
est2genome
fasta
ggsearch
glsearch
needle
stretcher
swat
Alignment > Graphical
blixem
clcsequenceviewer
clustalx
dotter
jalview
jprofilegrid
mummerplot
nucmer2xfig
seaview
squint
Alignment > Local
arb
bl2seq
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cross_match
dba
fasta
fastf
fastm
fasts
fastx
fasty
flalign
glsearch
lalign
lfasta
matcher
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prenuc
prfx
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psw
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seqmatchall
sibsim4
sim4
ssearch
supermatcher
swat
tfastf
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tfasts
tfastx
tfasty
water
wordfinder
wordmatch
Alignment > Multiple
annotate
clustalw
clustalx
combineMUMs
dialign
edialign
emma
exact-tandems
gaps
hmmalign
infoalign
jalview
lalign2list
mapview
mgaps
mocca
mummer
mummerplot
muscle
nucmer
nucmer2xfig
plotcon
postnuc
postpro
prank
prepro
prettyplot
PROmer
repeat-match
run-mummer1
run-mummer3
seaview
show-aligns
show-coords
show-tiling
showalign
squint
t-coffee
tranalign
yamap
Alignment > Profiles
jprofilegrid
profit
profit
prophecy
prophecy
prophet
prophet
Alignment > Statistics
alistat
pfscale
prfx
prss
weight
Clustering
Clustering > Graph
clmconf
clmdist
clmimac
clminfo
clmmeet
clmresidue
mcl
mcx
mcxconvert
mcxmap
mcxsubs
Clustering > Sequences
assembly-conversion-tools
blastclust
cd-hit
clobb
gap4
gcphrap
phrap
Databases
omssa
big-blast
Databases > Indexing
arb
formatdb
formatrpsdb
hmmindex
makeblastdb
makembindex
sindex
Databases > Post_search_graphical
mview
Databases > Post_search_processing
mspcrunch
mview
prfx
prss
Databases > Retrieval
afetch
arb
blastdbcmd
fastacmd
hmmfetch
maxdLoad2
sfetch
Databases > Searching
arb
big-blast
blast+
blast2
blastall
blastcl3
blastn
blastp
blastpgp
blastx
fasta
fastf
fastm
fasts
fastx
fasty
ggsearch
glsearch
hmmpfam
hmmpfam-pvm
hmmsearch
hmmsearch-pvm
impala
maxdLoad2
megablast
netblast
omssa
pfscan
pfsearch
psiblast
rpsblast
rpsblast+
rpstblastn
seedtop
ssearch
taxblast
tblastn
tblastx
tfastf
tfastm
tfasts
tfastx
tfasty
Databases > Submission_tools
sequin
Display
cn3d
textsearch
sixpack
showseq
showdb
seealso
remap
prettyseq
pepwheel
pepnet
lindna
cirdna
abiview
trev
Display > Alignments
boxshade
jprofilegrid
Display > Annotation
act
artemis
gff2ps
showfeat
Display > Dotplots
dotter
lalign
lav2ps
lav2svg
Display > Sequence_traces
consed
gap4
trev
Display > Structure
cn3d
rasmol
Edit
yank
vectorstrip
union
trimspac
trimseq
trimest
splitter
skipseq
skipredundan
seqrettype
seqretsplit
seqretset
seqretall
seqret
revseq
pasteseq
origunion
origsplitter
nthseq
notseq
nospac
noreturn
nohtm
newseq
maskseq
maskfeat
maskambigprot
maskambignuc
makeprotseq
makenucseq
listor
featreport
featcopy
extractseq
extractfeat
extractalign
entret
descseq
degapseq
cutseq
codcopy
biosed
aligncopypai
aligncopy
Enzyme_kinetics
findkm
Feature_tables
twofeat
coderet
Hmm
sreformat
sindex
shuffle
sfetch
hmmsearch-pvm
hmmsearch
hmmpfam-pvm
hmmpfam
hmmindex
hmmfetch
hmmemit
hmmconvert
hmmcalibrate-pvm
hmmcalibrate
hmmbuild
hmmalign
Information
wossname
whichdb
tfm
infoseq
inforesidu
infobas
Menus
Microarray
bioconductor
Microarray > Analysis
bioconductor
genespring
maxdLoad2
maxdview
Microarray > Annotation
bioconductor
Microarray > Graphical_views
bioconductor
genespring
maxdview
Microarray > Primers
OligoArray
Nucleic
Nucleic > 2d_structure
arb
einverted
garnier
helixturnhelix
hmoment
newcoils
pepcoil
pepnet
pepwheel
tmap
Nucleic > Annotation
act
artemis
partigene
Nucleic > Assembly
bwa
cap3
consed
gcphrap
mira
partigene
phrap
ssake
velvet
Nucleic > Base_calling
phred
pregap4
Nucleic > Codon_usage
cai
chips
codcmp
codon-usage
cusp
syco
Nucleic > Composition
backtranambig
backtranseq
banana
btwisted
chaos
charge
checktrans
complex
compseq
compseq
dan
density
emowse
freak
freak
get-len
giep
iep
isochore
mwcontam
mwfilter
octanol
pepinfo
pepstats
pepwindow
pepwindowall
sirna
wordcount
wordcount
Nucleic > Cpg_islands
cpgplot
cpgreport
geecee
newcpgreport
newcpgseek
Nucleic > Est
cd-hit-est
estscan
estwise
estwisedb
genewise
genewisedb
partigene
prot4est
sibsim4
sim4
trace2dbest
Nucleic > Gene_finding
act
anomaly
artemis
build-icm
check
codon-usage
compare-lists
estscan
estwise
estwisedb
extract
generate
genewise
genewisedb
get-putative
getorf
glimmer2
long-orfs
marscan
plotorf
prot4est
run-glimmer2
showorf
sibsim4
sim4
sixpack
syco
tcode
wobble
Nucleic > Graphical
act
artemis
Nucleic > Masking
dustmasker
segmasker
windowmasker
Nucleic > Motifs
antigenic
digest
dreg
epestfind
fuzznuc
fuzzpro
fuzztran
fuzztran
glam2
helixturnhelix
marscan
ocount
oddcomp
patmatdb
patmatmotifs
pepcoil
preg
pscan
sigcleave
Nucleic > Mutation
msbar
msbar
pregap4
shuffleseq
shuffleseq
Nucleic > Nextgen
bwa
caftools
consed
maq
mira
mira-3rd-party
roche2gap
samtools
ssake
tqs
velvet
Nucleic > Primers
eprimer3
OligoArray
prima
primer3
primers
primersearch
stssearch
Nucleic > Profiles
jprofilegrid
profit
profit
prophecy
prophecy
prophet
prophet
Nucleic > Repeats
cross_match
dust
dustmasker
einverted
equicktandem
etandem
mdust
palindrome
windowmasker
Nucleic > Restriction
recoder
redata
remap
restdist
restml
restover
restrict
showseq
silent
Nucleic > Transcription
jaspscan
tfscan
Nucleic > Translation
6ft
backtranambig
backtranseq
coderet
plotorf
prettyseq
remap
showorf
showseq
sixpack
tfastx
tfasty
transeq
Phylogeny
phylip
FastTree
mothur
evolver
Phylogeny > Bayesian
migrate
mrbayes
mrbayes-multi
Phylogeny > Clustering
dotur
Phylogeny > Consensus
consense
Phylogeny > Continuous_characters
contml
contrast
Phylogeny > Discrete_characters
clique
dollop
dolpenny
factor
mix
penny
Phylogeny > Distance_matrix
arb
fitch
kitsch
mothur
neighbor
Phylogeny > Gene_frequencies
gendist
Phylogeny > Maximum_likelihood
arb
baseml
basemlg
codeml
fastdnaml
mcmctree
pamp
Phyml
proml
PROmlk
restml
tree-puzzle
yn00
Phylogeny > Maximum_parsimony
dnamove
pars
Phylogeny > Misc
dendroscope
dolmove
drawgram
drawtree
embossdata
embossversion
entrails
Lamarc
mesquite
move
njplot
Phylogeny > Molecular_sequence
clustalw
clustalx
distmat
dnacomp
dnadist
dnainvar
dnaml
dnamlk
dnapars
dnapenny
protdist
protpars
seqboot
Phylogeny > Tree_drawing
ape
arb
atv
dendroscope
njplot
retree
splitstree
treedist
treeview
xsplits
Pipelines
Taverna
run-mummer3
nucmer
Pipelines > Sequence_assembly
gap4
partigene
stars
Pipelines > Sequence_processing
nucmer
pregap4
run-mummer3
stars
trace2dbest
Pipelines > Sequence_typing
stars
Pipelines > Workflows
Taverna
Protein
omssa
Protein > 2d_structure
arb
einverted
garnier
helixturnhelix
hmoment
newcoils
pepcoil
pepnet
pepwheel
tmap
Protein > 3d_structure
garlic
psiphi
rasmol
Protein > Composition
backtranambig
backtranseq
banana
btwisted
chaos
charge
checktrans
complex
compseq
compseq
dan
density
emowse
freak
freak
get-len
giep
iep
isochore
mwcontam
mwfilter
octanol
pepinfo
pepstats
pepwindow
pepwindowall
sirna
wordcount
wordcount
Protein > Dynamics
gromacs
Protein > Mapping
peptidemapper
Protein > Masking
dustmasker
segmasker
windowmasker
Protein > Motifs
antigenic
digest
dreg
epestfind
fuzznuc
fuzzpro
fuzztran
fuzztran
glam2
helixturnhelix
marscan
ocount
oddcomp
patmatdb
patmatmotifs
pepcoil
preg
pscan
sigcleave
Protein > Mutation
msbar
msbar
pregap4
shuffleseq
shuffleseq
Protein > Profiles
jprofilegrid
profit
profit
prophecy
prophecy
prophet
prophet
Statistics
mothur
Statistics > biodiversity
BiodiversityR
mothur
Statistics > General
chi2
R
Rcmdr
Statistics > Microarray
bioconductor
Statistics > Other_sequence
fasta
prfx
prss
seqstat
Statistics > qtl
BTmapqtl
Emap
Eqtl
JZmapqtl
LRmapqtl
MImapqtl
MultiRegress
Preplot
Prune
Qstats
QTLcart
QTL_Cartographer
Rcross
Rmap
Rqtl
SRmapqtl
Zmapqtl
Test
testplot
seqretsingle
seqretallfeat
seqinfo
patmattest
intconv
histogramtest
demotable
demostringnew
demostring
demolist
demofeatures
demoalign
corbatest
ajtest
ajfeatest
ajbad
Utils
biojava
extract_from_pdb
bioperl
Utils > Assembly reformatting
assembly-conversion-tools
caf2gap
caftools
gap2caf
mira-3rd-party
Utils > Database_creation
aaindexextract
cutgextract
jaspextract
printsextract
prosextract
rebaseextract
tfextract
Utils > Database_indexing
dbiblast
dbifasta
dbiflat
dbigcg
dbxfasta
dbxflat
dbxgcg
dbxstat
Utils > Misc
dendroscope
dolmove
drawgram
drawtree
embossdata
embossversion
entrails
Lamarc
mesquite
move
njplot
Utils > Sequence_cleaning
lucy
Utils > Sequence_info
extract_from_pdb
seqstat
Utils > Sequence_reformatting
2ft
clustalw
clustalx
copymat
extract_from_pdb
gtop
hmmconvert
htop
makemat
pfmake
psa2msa
ptof
ptoh
readseq
sfetch
sreformat
Utils > Software_development
bioconductor
biojava
bioperl
bioruby
