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Alignment
yamap
clcsequenceviewer
show-tiling
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run-mummer3
run-mummer1
repeat-match
PROmer
prepro
prenuc
postpro
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nucmer
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mummer
mgaps
mapview
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exact-tandems
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annotate
flalign
blixem
Alignment > Consensus
cons
gap4
megamerger
merger
spin
Alignment > Differences
act
diffseq
Alignment > Dot_plots
dotmatcher
dotpath
dotter
dottup
polydot
Alignment > Editing
clcsequenceviewer
jalview
Alignment > Global
est2genome
fasta
ggsearch
glsearch
needle
stretcher
swat
Alignment > Graphical
blixem
clcsequenceviewer
clustalx
dotter
jalview
mummerplot
nucmer2xfig
seaview
Alignment > Local
arb
bl2seq
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dba
fasta
fastf
fastm
fasts
fastx
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flalign
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matcher
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prss
psw
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ssearch
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swat
tfastf
tfastm
tfasts
tfastx
tfasty
water
wordmatch
Alignment > Multiple
annotate
clustalw
clustalx
combineMUMs
emma
exact-tandems
gaps
hmmalign
infoalign
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
t-coffee
tranalign
yamap
Alignment > Profiles
pfmake
pfsearch
pftools
psa2msa
ptof
ptoh
Alignment > Statistics
alistat
pfscale
prfx
prss
weight
Clustering
cd-hit
Clustering > Graph
clmconf
clmdist
clmimac
clminfo
clmmeet
clmresidue
mcl
mcx
mcxconvert
mcxmap
mcxsubs
Clustering > Sequences
assembly-conversion-tools
blastclust
cd-hit
cd-hit-est
clobb
gap4
gcphrap
phrap
Databases
omssa
big-blast
Databases > Indexing
arb
formatdb
hmmindex
sindex
Databases > Post_search_graphical
mview
Databases > Post_search_processing
mspcrunch
mview
prfx
prss
Databases > Retrieval
afetch
arb
fastacmd
hmmfetch
maxdLoad2
sfetch
Databases > Searching
arb
big-blast
blastall
blastcl3
blastpgp
fasta
fastf
fastm
fasts
fastx
fasty
ggsearch
glsearch
hmmpfam
hmmpfam-pvm
hmmsearch
hmmsearch-pvm
impala
maxdLoad2
megablast
netblast
omssa
pfscan
pfsearch
rpsblast
seedtop
ssearch
tfastf
tfastm
tfasts
tfastx
tfasty
Databases > Submission_tools
sequin
Display
trev
textsearch
sixpack
showseq
showfeat
showdb
seealso
remap
prettyseq
pepwheel
pepnet
lindna
cirdna
abiview
showalign
prettyplot
Display > Dotplots
dotmatcher
dotter
lalign
lav2ps
lav2svg
Display > Sequence_traces
consed
gap4
trev
Display > Structure
rasmol
Edit
yank
vectorstrip
union
trimseq
trimest
splitter
skipseq
seqretsplit
seqret
revseq
pasteseq
nthseq
notseq
noreturn
newseq
maskseq
maskfeat
listor
extractseq
extractfeat
entret
descseq
degapseq
cutseq
biosed
Enzyme_kinetics
findkm
Feature_tables
twofeat
coderet
maskfeat
extractfeat
showfeat
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
textsearch
showdb
seealso
infoalign
Menus
Microarray
bioconductor
Microarray > Analysis
bioconductor
genespring
maxdLoad2
maxdview
Microarray > Annotation
bioconductor
Microarray > Graphical_views
bioconductor
genespring
maxdview
Microarray > Primers
OligoArray
Nucleic
ocount
run-glimmer2
long-orfs
glimmer2
get-putative
get-len
generate
extract
compare-lists
codon-usage
check
build-icm
anomaly
restdist
Nucleic > 2d_structure
arb
einverted
Nucleic > Annotation
act
artemis
partigene
Nucleic > Assembly
cap3
consed
gcphrap
partigene
phrap
Nucleic > Base_calling
phred
pregap4
Nucleic > Codon_usage
cai
chips
codcmp
codon-usage
cusp
syco
Nucleic > Composition
banana
btwisted
chaos
compseq
dan
freak
get-len
isochore
sirna
wordcount
Nucleic > Cpg_islands
cpgplot
cpgreport
geecee
newcpgreport
newcpgseek
Nucleic > Est
cd-hit-est
ESTFerret
estscan
estwise
estwisedb
genewise
genewisedb
partigene
prot4est
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
sixpack
syco
tcode
wobble
Nucleic > Graphical
act
artemis
Nucleic > Motifs
dreg
fuzznuc
fuzztran
marscan
ocount
Nucleic > Mutation
msbar
pregap4
shuffleseq
Nucleic > Primers
eprimer3
OligoArray
primer3
primersearch
stssearch
Nucleic > Profiles
profit
prophecy
prophet
Nucleic > Repeats
cross_match
einverted
equicktandem
etandem
palindrome
Nucleic > Restriction
recoder
redata
remap
restdist
restml
restover
restrict
showseq
silent
Nucleic > Transcription
tfscan
Nucleic > Translation
6ft
backtranseq
coderet
plotorf
prettyseq
remap
showorf
showseq
sixpack
tfastx
tfasty
transeq
Phylogeny
Phyml
migrate
Lamarc
dendroscope
ape
evolver
dnamove
Phylogeny > Bayesian
migrate
mrbayes
Phylogeny > Clustering
dotur
Phylogeny > Consensus
consense
Phylogeny > Continuous_characters
contml
contrast
Phylogeny > Discrete_characters
clique
dollop
dolpenny
factor
mix
penny
Phylogeny > Distance_matrix
arb
distmat
fitch
kitsch
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
ape
arb
dendroscope
dolmove
drawgram
drawtree
Lamarc
mesquite
move
njplot
Phylogeny > Molecular_sequence
clustalw
clustalx
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
cd-hit
omssa
Protein > 2d_structure
garnier
helixturnhelix
hmoment
pepcoil
pepnet
pepwheel
tmap
Protein > 3d_structure
rasmol
Protein > Composition
backtranseq
charge
checktrans
compseq
emowse
fastf
fastm
fasts
freak
iep
mwcontam
mwfilter
octanol
omssa
pepinfo
pepstats
pepwindow
pepwindowall
tfastf
tfasts
Protein > Mapping
peptidemapper
Protein > Motifs
antigenic
digest
fuzzpro
fuzztran
helixturnhelix
oddcomp
patmatdb
patmatmotifs
pepcoil
preg
pscan
sigcleave
Protein > Mutation
msbar
shuffleseq
Protein > Profiles
profit
prophecy
prophet
Statistics
Statistics > General
chi2
R
Statistics > Microarray
bioconductor
Statistics > Multiple_alignment
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
Utils
extract_from_pdb
embossdata
bioperl
Utils > Assembly reformatting
assembly-conversion-tools
Utils > Database_creation
cutgextract
printsextract
prosextract
rebaseextract
tfextract
Utils > Database_indexing
dbiblast
dbifasta
dbiflat
dbigcg
Utils > Misc
bioperl
embossdata
extract_from_pdb
mesquite
pedro
seqsplit
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
seqret
sfetch
sreformat
Utils > Software_development
bioconductor
bioperl
bioruby
