.:
.
..
emboss
embossdir.txt

./emboss:
.
..
bin
EMBOSS-2.5.1
EMBOSS-2.5.1.tar.gz
EMBOSS-GUI
EMBOSS-GUI.tar.gz
EMNU-1.0.5.tar.gz
ESIM4-1.0.0.tar.gz
gbacc.idx.gz
gbsdr.txt.gz
genpept.fsa.gz
HMMER-2.1.1.tar.gz
lib
MEME-2.3.1.tar.gz
MSE-0.0.4.tar.gz
PHYLIP-3.573c.tar.gz
share
TOPO-0.1.tar.gz

./emboss/bin:
.
..
ealistat
eclique
econsense
econtml
econtrast
ednacomp
ednadist
ednainvar
ednaml
ednamlk
ednapars
ednapenny
edollop
edolpenny
efactor
efitch
egendist
ehmmalign
ehmmbuild
ehmmcalibrate
ehmmconvert
ehmmemit
ehmmfetch
ehmmindex
ehmmpfam
ehmmsearch
ekitsch
emix
eneighbor
epenny
eprotdist
eprotpars
erestml
eseqboot
topo

./emboss/EMBOSS-2.5.1:
.
..
aclocal.m4
ajax
AUTHORS
bin
ChangeLog
COMPAT
config.guess
config.log
config.status
config.sub
configure
configure.in
COPYING
depcomp
doc
embassy
emboss
FAQ
INSTALL
install-sh
jemboss
KNOWN_BUGS
libtool
LICENSE
ltmain.sh
Makefile
Makefile.am
Makefile.in
missing
mkinstalldirs
NEWS
nucleus
ONEWS
plplot
PROBLEMS
README
scripts
share
test
THANKS

./emboss/EMBOSS-2.5.1/ajax:
.
..
ajacd.c
ajacd.h
ajacd.lo
ajacd.o
ajalign.c
ajalign.h
ajalign.lo
ajalign.o
ajarch.h
ajarr.c
ajarr.h
ajarr.lo
ajarr.o
ajassert.c
ajassert.h
ajassert.lo
ajassert.o
ajax.h
ajbase.c
ajbase.h
ajbase.lo
ajbase.o
ajcall.c
ajcall.h
ajcall.lo
ajcall.o
ajcod.c
ajcod.h
ajcod.lo
ajcod.o
ajcorba.c
ajcorbaembl.h
ajcorbaemc.c
ajcorbaemc.lo
ajcorbaemc.o
ajcorbaems.c
ajcorbaems.lo
ajcorbaems.o
ajcorba.h
ajcorba.lo
ajcorba.o
ajdan.c
ajdan.h
ajdan.lo
ajdan.o
ajdefine.h
ajexcept.c
ajexcept.h
ajexcept.lo
ajexcept.o
ajfeat.c
ajfeatdata.h
ajfeat.h
ajfeat.lo
ajfeat.o
ajfile.c
ajfile.h
ajfile.lo
ajfile.o
ajfmt.c
ajfmt.h
ajfmt.lo
ajfmt.o
ajgraph.c
ajgraph.h
ajgraph.lo
ajgraph.o
ajgraphstruct.h
ajhist.c
ajhist.h
ajhist.lo
ajhist.o
ajjava.c
ajjava.h
ajjava.lo
ajjava.o
ajlist.c
ajlist.h
ajlist.lo
ajlist.o
ajmath.c
ajmath.h
ajmath.lo
ajmath.o
ajmatrices.c
ajmatrices.h
ajmatrices.lo
ajmatrices.o
ajmem.c
ajmem.h
ajmem.lo
ajmem.o
ajmess.c
ajmess.h
ajmess.lo
ajmess.o
ajnam.c
ajnam.h
ajnam.lo
ajnam.o
ajposreg.c
ajposreg.h
ajposreg.lo
ajposreg.o
ajrange.c
ajrange.h
ajrange.lo
ajrange.o
ajreg.c
ajreg.h
ajreg.lo
ajreg.o
ajreport.c
ajreport.h
ajreport.lo
ajreport.o
ajseqabi.c
ajseqabi.h
ajseqabi.lo
ajseqabi.o
ajseq.c
ajseqdata.h
ajseqdb.c
ajseqdb.h
ajseqdb.lo
ajseqdb.o
ajseq.h
ajseq.lo
ajseq.o
ajseqread.c
ajseqread.h
ajseqread.lo
ajseqread.o
ajseqtype.c
ajseqtype.h
ajseqtype.lo
ajseqtype.o
ajseqwrite.c
ajseqwrite.h
ajseqwrite.lo
ajseqwrite.o
ajsort.c
ajsort.h
ajsort.lo
ajsort.o
ajstr.c
ajstr.h
ajstr.lo
ajstr.o
ajsys.c
ajsys.h
ajsys.lo
ajsys.o
ajtable.c
ajtable.h
ajtable.lo
ajtable.o
ajtime.c
ajtime.h
ajtime.lo
ajtime.o
ajtranslate.c
ajtranslate.h
ajtranslate.lo
ajtranslate.o
ajutil.c
ajutil.h
ajutil.lo
ajutil.o
ajxyz.c
ajxyz.h
ajxyz.lo
ajxyz.o
COPYING
.deps
hsp_cclass.h
hsp_cname.h
hsp_debug.c
hsp_debug.lo
hsp_debug.o
hsp_engine.c
hsp_engine.h
hsp_regcomp.c
hsp_regcomp.h
hsp_regcomp.lo
hsp_regcomp.o
hsp_regerror.c
hsp_regerror.h
hsp_regerror.lo
hsp_regerror.o
hsp_regex2.h
hsp_regexec.c
hsp_regexec.lo
hsp_regexec.o
hsp_regex.h
hsp_regfree.c
hsp_regfree.lo
hsp_regfree.o
hsp_split.c
hsp_split.lo
hsp_split.o
hsp_utils.h
hsregerror.c
hsregerror.lo
hsregerror.o
hsregexp.c
hsregexp.h
hsregexp.lo
hsregexp.o
hsregmagic.h
hsregsub.c
hsregsub.lo
hsregsub.o
libajaxg.la
libajax.la
.libs
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/ajax/.deps:
.
..
ajacd.Plo
ajalign.Plo
ajarr.Plo
ajassert.Plo
ajbase.Plo
ajcall.Plo
ajcod.Plo
ajcorbaemc.Plo
ajcorbaems.Plo
ajcorba.Plo
ajdan.Plo
ajexcept.Plo
ajfeat.Plo
ajfile.Plo
ajfmt.Plo
ajgraph.Plo
ajhist.Plo
ajjava.Plo
ajlist.Plo
ajmath.Plo
ajmatrices.Plo
ajmem.Plo
ajmess.Plo
ajnam.Plo
ajposreg.Plo
ajrange.Plo
ajreg.Plo
ajreport.Plo
ajseqabi.Plo
ajseqdb.Plo
ajseq.Plo
ajseqread.Plo
ajseqtype.Plo
ajseqwrite.Plo
ajsort.Plo
ajstr.Plo
ajsys.Plo
ajtable.Plo
ajtime.Plo
ajtranslate.Plo
ajutil.Plo
ajxyz.Plo
hsp_debug.Plo
hsp_regcomp.Plo
hsp_regerror.Plo
hsp_regexec.Plo
hsp_regfree.Plo
hsp_split.Plo
hsregerror.Plo
hsregexp.Plo
hsregsub.Plo

./emboss/EMBOSS-2.5.1/ajax/.libs:
.
..
libajax.a
libajaxg.a
libajaxg.la
libajaxg.lai
libajaxg.so
libajaxg.so.0
libajaxg.so.0.1.0
libajax.la
libajax.lai
libajax.so
libajax.so.0
libajax.so.0.1.0

./emboss/EMBOSS-2.5.1/bin:
.
..
eclique
econsense
econtml
econtrast
ednacomp
ednadist
ednainvar
ednaml
ednamlk
ednapars
ednapenny
edollop
edolpenny
efactor
efitch
egendist
ekitsch
emix
eneighbor
epenny
eprotdist
eprotpars
erestml
eseqboot

./emboss/EMBOSS-2.5.1/doc:
.
..
images
Makefile
Makefile.am
Makefile.in
manuals
programs
tutorials

./emboss/EMBOSS-2.5.1/doc/images:
.
..
e140x45.jpg
e150x48.jpg
e200x64.jpg
e300x97.jpg
e400x129.jpg

./emboss/EMBOSS-2.5.1/doc/manuals:
.
..
admin.aux
admin.dvi
adminguide.tar.gz
admin.log
admin.pdf
admin.ps
admin.sty
admin.tex
admin.toc
EMBOSS-FreeBSD-HOWTO.txt
emboss_qg.pdf
emboss_qg.ps
emboss.sty
fdl.txt
internals-access.txt
internals-indexing.txt
internals-query.txt
internals-seqin.txt
Makefile
Makefile.am
Makefile.in
program.ps.gz

./emboss/EMBOSS-2.5.1/doc/programs:
.
..
emboss_icon.gif
emboss_icon.jpg
html
Makefile
Makefile.am
Makefile.in
text

./emboss/EMBOSS-2.5.1/doc/programs/html:
.
..
aaindexextract.html
abiview0.gif
abiview.html
ajtest.html
alignment_consensus_group.html
alignment_differences_group.html
alignment_dot_plots_group.html
alignment_global_group.html
alignment_local_group.html
alignment_multiple_group.html
alignwrap.html
antigenic.html
backtranseq.html
banana0.gif
banana.html
biosed.html
btwisted.html
cai.html
chaos0.gif
chaos.html
charge.html
checktrans.html
chips.html
cirdna.gif
cirdna.html
clique.html
codcmp.html
coderet.html
compseq.html
consense.html
cons.html
contacts.html
contml.html
contrast.html
cpgplot0.gif
cpgplot.html
cpgreport.html
cusp.html
cutgextract.html
cutseq.html
dan.html
dbiblast.html
dbifasta.html
dbiflat.html
dbigcg.html
degapseq.html
descseq.html
dichet.html
diffseq.html
digest.html
display_group.html
distmat.html
dnacomp.html
dnadist.html
dnainvar.html
dnaml.html
dnamlk.html
dnapars.html
dnapenny.html
dollop.html
dolpenny.html
domainer.html
dotmatcher0.gif
dotmatcher.html
dotpath.html
dottup0.gif
dottup.html
dreg.html
eclique.html
econsense.html
econtml.html
econtrast.html
edit_group.html
ednacomp.html
ednadist.html
ednainvar.html
ednaml.html
ednamlk.html
ednapars.html
ednapenny.html
edollop.html
edolpenny.html
efactor.html
efitch.html
egendist.html
einverted.html
ekitsch.html
embossdata.html
emboss_icon.gif
emboss_icon.jpg
embossversion.html
emix.html
emma.html
emowse.html
eneighbor.html
entret.html
enzyme_kinetics_group.html
epenny.html
eprimer3.html
eprotdist.html
eprotpars.html
equicktandem.html
erestml.html
eseqboot.html
est2genome.html
etandem.html
extractfeat.html
extractseq.html
factor.html
feature_tables_group.html
findkm0.gif
findkm.html
fitch.html
freak.html
funky.html
fuzznuc.html
fuzzpro.html
fuzztran.html
garnier.html
geecee.html
gendist.html
getorf.html
groups.html
helixturnhelix.html
hetparse.html
histogramtest.html
hmmgen.html
hmoment.html
iep.html
index.html
infoalign.html
information_group.html
infoseq.html
interface.html
isochore0.gif
isochore.html
jembossctl.html
kitsch.html
lindna.gif
lindna.html
listor.html
Makefile
Makefile.am
Makefile.in
marscan.html
maskfeat.html
maskseq.html
matcher.html
megamerger.html
menus_group.html
merger.html
mix.html
msbar.html
mse.html
mwcontam.html
mwfilter.html
needle.html
neighbor.html
newcpgreport.html
newcpgseek.html
newseq.html
noreturn.html
notseq.html
nrscope.html
nthseq.html
nucleic_2d_structure_group.html
nucleic_codon_usage_group.html
nucleic_composition_group.html
nucleic_cpg_islands_group.html
nucleic_gene_finding_group.html
nucleic_motifs_group.html
nucleic_mutation_group.html
nucleic_primers_group.html
nucleic_profiles_group.html
nucleic_repeats_group.html
nucleic_restriction_group.html
nucleic_transcription_group.html
nucleic_translation_group.html
octanol0.gif
octanol.html
oddcomp.html
palindrome.html
pasteseq.html
patmatdb.html
patmatmotifs.html
pdbparse.html
pdbtosp.html
penny.html
pepcoil.html
pepinfo1.gif
pepinfo2.gif
pepinfo.html
pepnet0.gif
pepnet.html
pepstats.html
pepwheel0.gif
pepwheel.html
pepwindow0.gif
pepwindowall0.gif
pepwindowall.html
pepwindow.html
phylogeny_group.html
plotcon.html
plotorf0.gif
plotorf.html
polydot0.gif
polydot.html
preg.html
prettyplot3.gif
prettyplot4.gif
prettyplot.html
prettyseq.html
primersearch.html
printsextract.html
profgen.html
profit.html
prophecy.html
prophet.html
prosextract.html
protdist.html
protein_2d_structure_group.html
protein_3d_structure_group.html
protein_composition_group.html
protein_motifs_group.html
protein_mutation_group.html
protein_profiles_group.html
protein_structure_group.html
pscan.html
psiblasts.html
rebaseextract.html
recode.html
recoder.html
redata.html
remap.html
restml.html
restover.html
restrict.html
revseq.html
scopalign.html
scope.html
scopnr.html
scopparse.html
scoprep.html
scopreso.html
scopseqs.html
seealso.html
seqalign.html
seqboot.html
seqmatchall.html
seqnr.html
seqretallfeat.html
seqretall.html
seqretfeat.html
seqret.html
seqretset.html
seqretsplit.html
seqsearch.html
seqsort.html
seqwords.html
showalign.html
showdb.html
showfeat.html
showorf.html
showseq.html
shuffleseq.html
sigcleave.html
siggen.html
sigscan.html
silent.html
skipseq.html
splitter.html
stamps.html
stretcher.html
stssearch.html
supermatcher.html
swissparse.html
syco0.gif
syco1.gif
syco.html
test_group.html
textsearch.html
tfextract.html
tfm.html
tfscan.html
tmap0.gif
tmap.html
topo.gif
topo.html
tranalign.html
transeq.html
trimest.html
trimseq.html
union.html
utils_database_creation_group.html
utils_database_indexing_group.html
utils_misc_group.html
vectorstrip.html
water.html
whichdb.html
wobble0.gif
wobble.html
wordcount.html
wordmatch.html
wossname.html
yank.html

./emboss/EMBOSS-2.5.1/doc/programs/text:
.
..
aaindexextract.txt
abiview.txt
ajtest.txt
alignwrap.txt
antigenic.txt
backtranseq.txt
banana.txt
biosed.txt
btwisted.txt
cai.txt
chaos.txt
charge.txt
checktrans.txt
chips.txt
cirdna.txt
clique.txt
codcmp.txt
coderet.txt
complex.txt
compseq.txt
consense.txt
cons.txt
contacts.txt
contml.txt
contrast.txt
cpgplot.txt
cpgreport.txt
cusp.txt
cutgextract.txt
cutseq.txt
dan.txt
dbiblast.txt
dbifasta.txt
dbiflat.txt
dbigcg.txt
degapseq.txt
descseq.txt
dichet.txt
diffseq.txt
digest.txt
distmat.txt
dnacomp.txt
dnadist.txt
dnainvar.txt
dnamlk.txt
dnaml.txt
dnapars.txt
dnapenny.txt
dollop.txt
dolpenny.txt
domainer.txt
dotmatcher.txt
dotpath.txt
dottup.txt
dreg.txt
eclique.txt
econsense.txt
econtml.txt
econtrast.txt
ednacomp.txt
ednadist.txt
ednainvar.txt
ednamlk.txt
ednaml.txt
ednapars.txt
ednapenny.txt
edollop.txt
edolpenny.txt
efactor.txt
efitch.txt
egendist.txt
einverted.txt
ekitsch.txt
embossdata.txt
embossversion.txt
emix.txt
emma.txt
emowse.txt
eneighbor.txt
entret.txt
epenny.txt
eprimer3.txt
eprotdist.txt
eprotpars.txt
equicktandem.txt
erestml.txt
eseqboot.txt
est2genome.txt
etandem.txt
extractfeat.txt
extractseq.txt
factor.txt
findkm.txt
fitch.txt
freak.txt
funky.txt
fuzznuc.txt
fuzzpro.txt
fuzztran.txt
garnier.txt
geecee.txt
gendist.txt
getorf.txt
groups.txt
helixturnhelix.txt
hetparse.txt
histogramtest.txt
hmmgen.txt
hmoment.txt
iep.txt
infoalign.txt
infoseq.txt
interface.txt
isochore.txt
jembossctl.txt
kitsch.txt
lindna.txt
listor.txt
Makefile
Makefile.am
Makefile.in
marscan.txt
maskfeat.txt
maskseq.txt
matcher.txt
megamerger.txt
merger.txt
mix.txt
msbar.txt
mse.txt
mwcontam.txt
mwfilter.txt
needle.txt
neighbor.txt
newcpgreport.txt
newcpgseek.txt
newseq.txt
noreturn.txt
notseq.txt
nrscope.txt
nthseq.txt
octanol.txt
oddcomp.txt
palindrome.txt
pasteseq.txt
patmatdb.txt
patmatmotifs.txt
pdbparse.txt
pdbtosp.txt
penny.txt
pepcoil.txt
pepinfo.txt
pepnet.txt
pepstats.txt
pepwheel.txt
pepwindowall.txt
pepwindow.txt
plotcon.txt
plotorf.txt
polydot.txt
preg.txt
prettyplot.txt
prettyseq.txt
primersearch.txt
printsextract.txt
profgen.txt
profit.txt
prophecy.txt
prophet.txt
prosextract.txt
protdist.txt
pscan.txt
psiblasts.txt
rebaseextract.txt
recoder.txt
recode.txt
redata.txt
remap.txt
restml.txt
restover.txt
restrict.txt
revseq.txt
scopalign.txt
scope.txt
scopnr.txt
scopparse.txt
scoprep.txt
scopreso.txt
scopseqs.txt
seealso.txt
seqalign.txt
seqboot.txt
seqmatchall.txt
seqnr.txt
seqretallfeat.txt
seqretall.txt
seqretfeat.txt
seqretset.txt
seqretsplit.txt
seqret.txt
seqsearch.txt
seqsort.txt
seqwords.txt
showalign.txt
showdb.txt
showfeat.txt
showorf.txt
showseq.txt
shuffleseq.txt
sigcleave.txt
siggen.txt
sigscan.txt
silent.txt
SITE-DIRECTED.txt
skipseq.txt
splitter.txt
stamps.txt
stretcher.txt
stssearch.txt
supermatcher.txt
swissparse.txt
syco.txt
textsearch.txt
tfextract.txt
tfm.txt
tfscan.txt
tmap.txt
topo.txt
tranalign.txt
transeq.txt
trimest.txt
trimseq.txt
union.txt
vectorstrip.txt
water.txt
whichdb.txt
wobble.txt
wordcount.txt
wordmatch.txt
wossname.txt
yank.txt

./emboss/EMBOSS-2.5.1/doc/tutorials:
.
..
biblio.bib
dottup.ps.gz
emboss-gcg.ppt
emboss-interfaces.ppt
emboss-talk.ppt
emboss_tutorial.ps.gz
emboss_tutorial.tex
Makefile
Makefile.am
Makefile.in
pepinfo1.ps.gz
pepinfo2.ps.gz
plotorf.ps.gz
tmap.ps.gz

./emboss/EMBOSS-2.5.1/embassy:
.
..
HMMER-2.1.1
MEME-2.3.1
MSE-0.0.4
PHYLIP-3.573c
TOPO-0.1

./emboss/EMBOSS-2.5.1/embassy/HMMER-2.1.1:
.
..
aclocal.m4
AUTHORS
ChangeLog
config.log
config.status
configure
configure.in
COPYING
depcomp
emboss_acd
INSTALL
libtool
ltmain.sh
Makefile
Makefile.am
Makefile.in
NEWS
README
src

./emboss/EMBOSS-2.5.1/embassy/HMMER-2.1.1/emboss_acd:
.
..
ealistat.acd
ehmmalign.acd
ehmmbuild.acd
ehmmcalibrate.acd
ehmmconvert.acd
ehmmemit.acd
ehmmfetch.acd
ehmmindex.acd
ehmmpfam.acd
ehmmsearch.acd
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/embassy/HMMER-2.1.1/src:
.
..
aligneval.c
aligneval.lo
aligneval.o
alignio.c
alignio.lo
alignio.o
alphabet.c
alphabet.lo
alphabet.o
cluster.c
cluster.lo
cluster.o
config.h
core_algorithms.c
core_algorithms.lo
core_algorithms.o
dayhoff.c
dayhoff.lo
dayhoff.o
debug.c
debug.lo
debug.o
.deps
ealistat
ealistat.c
ealistat.o
ehmmalign
ehmmalign.c
ehmmalign.o
ehmmbuild
ehmmbuild.c
ehmmbuild.o
ehmmcalibrate
ehmmcalibrate.c
ehmmcalibrate.o
ehmmconvert
ehmmconvert.c
ehmmconvert.o
ehmmemit
ehmmemit.c
ehmmemit.o
ehmmfetch
ehmmfetch.c
ehmmfetch.o
ehmmindex
ehmmindex.c
ehmmindex.o
ehmmpfam
ehmmpfam.c
ehmmpfam.o
ehmmsearch
ehmmsearch.c
ehmmsearch.o
emit.c
emit.lo
emit.o
emulation.c
emulation.lo
emulation.o
file.c
file.lo
file.o
funcs.h
getopt.c
getopt.lo
getopt.o
globals.h
gnuregex.h
gsi.c
gsi.lo
gsi.o
histogram.c
histogram.lo
histogram.o
hmmio.c
hmmio.lo
hmmio.o
hsregex.c
hsregex.lo
hsregex.o
interleaved.c
interleaved.lo
interleaved.o
iupac.c
iupac.lo
iupac.o
libhmmer.la
.libs
Makefile
Makefile.am
Makefile.in
masks.c
masks.lo
masks.o
mathsupport.c
mathsupport.lo
mathsupport.o
misc.c
misc.lo
misc.o
modelmakers.c
modelmakers.lo
modelmakers.o
msf.c
msf.lo
msf.o
plan7.c
plan7.lo
plan7.o
plan9.c
plan9.lo
plan9.o
prior.c
prior.lo
prior.o
revcomp.c
revcomp.lo
revcomp.o
selex.c
selex.lo
selex.o
sqerror.c
sqerror.lo
sqerror.o
sqfuncs.h
sqio.c
sqio.lo
sqio.o
squid.h
sre_ctype.c
sre_ctype.lo
sre_ctype.o
sre_math.c
sre_math.lo
sre_math.o
sre_string.c
sre_string.lo
sre_string.o
stack.c
stack.lo
stack.o
structs.h
threads.c
threads.lo
threads.o
tophits.c
tophits.lo
tophits.o
trace.c
trace.lo
trace.o
translate.c
translate.lo
translate.o
types.c
types.lo
types.o
version.h
weight.c
weight.lo
weight.o

./emboss/EMBOSS-2.5.1/embassy/HMMER-2.1.1/src/.deps:
.
..
aligneval.Plo
alignio.Plo
alphabet.Plo
cluster.Plo
core_algorithms.Plo
dayhoff.Plo
debug.Plo
ealistat.Po
ehmmalign.Po
ehmmbuild.Po
ehmmcalibrate.Po
ehmmconvert.Po
ehmmemit.Po
ehmmfetch.Po
ehmmindex.Po
ehmmpfam.Po
ehmmsearch.Po
emit.Plo
emulation.Plo
file.Plo
getopt.Plo
gsi.Plo
histogram.Plo
hmmio.Plo
hsregex.Plo
interleaved.Plo
iupac.Plo
masks.Plo
mathsupport.Plo
misc.Plo
modelmakers.Plo
msf.Plo
plan7.Plo
plan9.Plo
prior.Plo
revcomp.Plo
selex.Plo
sqerror.Plo
sqio.Plo
sre_ctype.Plo
sre_math.Plo
sre_string.Plo
stack.Plo
threads.Plo
tophits.Plo
trace.Plo
translate.Plo
types.Plo
weight.Plo

./emboss/EMBOSS-2.5.1/embassy/HMMER-2.1.1/src/.libs:
.
..
ealistat
ehmmalign
ehmmbuild
ehmmcalibrate
ehmmconvert
ehmmemit
ehmmfetch
ehmmindex
ehmmpfam
ehmmsearch
libhmmer.a
libhmmer.la
libhmmer.lai
libhmmer.so
libhmmer.so.1
libhmmer.so.1.1.1

./emboss/EMBOSS-2.5.1/embassy/MEME-2.3.1:
.
..
aclocal.m4
AUTHORS
ChangeLog
configure
configure.in
COPYING
copyright
depcomp
emboss_acd
INSTALL
ltmain.sh
Makefile.am
Makefile.in
NEWS
README
src

./emboss/EMBOSS-2.5.1/embassy/MEME-2.3.1/emboss_acd:
.
..
Makefile
Makefile.am
Makefile.in
meme.acd

./emboss/EMBOSS-2.5.1/embassy/MEME-2.3.1/src:
.
..
align.c
banner.c
chi.c
clock.c
diagram.c
display.c
em.c
gamma.c
hash_alph.c
hash.c
INCLUDE
init.c
justlike.c
likelihood.c
logodds.c
logs.c
Makefile.am
Makefile.in
meme.c
meme_util.c
message.c
mp.c
normalize.c
oops.c
palindrome.c
prior.c
read_seq_file.c
regress.c
seq2theta.c
shorten.c
split.c
starts.c
subseq7.c
tcm.c
zoops.c

./emboss/EMBOSS-2.5.1/embassy/MEME-2.3.1/src/INCLUDE:
.
..
align.h
banner.h
chi.h
clock.h
curves.h
diagram.h
display.h
em.h
gamma.h
general.h
hash_alph.h
hash.h
histogram.h
logodds.h
logs.h
macros.h
Makefile.am
Makefile.in
mast.h
meme-cs.h
meme.h
message.h
motifnormal.h
motifs.h
mp.h
mtype.h
nrutil.h
prior.h
ProfileNormal.h
projrel.h
read_seq_file.h
readwrite.h
regress.h
rtarray.h
shuffle_int.h
split.h
user.h

./emboss/EMBOSS-2.5.1/embassy/MSE-0.0.4:
.
..
aclocal.m4
AUTHORS
ChangeLog
ckit
configure
configure.in
COPYING
depcomp
emboss_acd
h
INSTALL
LICENSE
ltmain.sh
Makefile.am
Makefile.in
NEWS
README
source

./emboss/EMBOSS-2.5.1/embassy/MSE-0.0.4/ckit:
.
..
datafiles.c
gcg.c
Makefile.am
Makefile.in
next.c
nextseqentry.c
pir.c
readentry.c
seqentry.c
seqspec.c
sequence.c
strings.c
ttyinterface.c
vdb.c
vms2.c

./emboss/EMBOSS-2.5.1/embassy/MSE-0.0.4/emboss_acd:
.
..
Makefile
Makefile.am
Makefile.in
mse.acd

./emboss/EMBOSS-2.5.1/embassy/MSE-0.0.4/h:
.
..
boolean.h
ckit.h
ckittypes.h
error.h
gcgdefines.h
kit.h
macros.h
Makefile.am
Makefile.in
mse.h
mwsevtmgr.h
mws.h
seqdef.h
seqentry.h
seqspec.h
seqsymbols.h
smgmacros.h
ttyinterface.h

./emboss/EMBOSS-2.5.1/embassy/MSE-0.0.4/source:
.
..
Makefile.am
Makefile.in
mse.c

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c:
.
..
aclocal.m4
AUTHORS
ChangeLog
config.log
config.status
configure
configure.in
COPYING
depcomp
doc
emboss_acd
include
INSTALL
libtool
ltmain.sh
Makefile
Makefile.am
Makefile.in
NEWS
README
src

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c/doc:
.
..
clique.doc
consense.doc
contchar.doc
contml.doc
contrast.doc
discrete.doc
distance.doc
dnacomp.doc
dnadist.doc
dnainvar.doc
dnaml.doc
dnamlk.doc
dnamove.doc
dnapars.doc
dnapenny.doc
dollop.doc
dolmove.doc
dolpenny.doc
draw.doc
drawgram.doc
drawtree.doc
factor.doc
fitch.doc
gendist.doc
kitsch.doc
main.doc
makeinf.doc
mix.doc
move.doc
neighbor.doc
penny.doc
protdist.doc
protml.doc
protpars.doc
restml.doc
retree.doc
seqboot.doc
sequence.doc

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c/emboss_acd:
.
..
codes.english
eclique.acd
econsense.acd
econtml.acd
econtrast.acd
ednacomp.acd
ednadist.acd
ednainvar.acd
ednaml.acd
ednamlk.acd
ednapars.acd
ednapenny.acd
edollop.acd
edolpenny.acd
efactor.acd
efitch.acd
egendist.acd
ekitsch.acd
emix.acd
eneighbor.acd
epenny.acd
eprotdist.acd
eprotpars.acd
erestml.acd
eseqboot.acd
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c/include:
.
..
drawgraphics.h
interface.h
phylip.h

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c/src:
.
..
clique.c
clique.o
consense.c
consense.o
contml.c
contml.o
contrast.c
contrast.o
.deps
dnacomp.c
dnacomp.o
dnadist.c
dnadist.o
dnainvar.c
dnainvar.o
dnaml2.c
dnaml2.o
dnaml.c
dnamlk2.c
dnamlk2.o
dnamlk.c
dnamlk.o
dnaml.o
dnapars.c
dnapars.o
dnapenny.c
dnapenny.o
dollop.c
dollop.o
dolpenny.c
dolpenny.o
eclique
econsense
econtml
econtrast
ednacomp
ednadist
ednainvar
ednaml
ednamlk
ednapars
ednapenny
edollop
edolpenny
efactor
efitch
egendist
ekitsch
emix
eneighbor
epenny
eprotdist
eprotpars
erestml
eseqboot
factor.c
factor.o
fitch.c
fitch.o
gendist.c
gendist.o
kitsch.c
kitsch.o
.libs
Makefile
Makefile.am
Makefile.in
mix2.c
mix2.o
mix.c
mix.o
neighbor.c
neighbor.o
penny.c
penny.o
protdist.c
protdist.o
protpars.c
protpars.o
restml2.c
restml2.o
restml.c
restml.o
seqboot.c
seqboot.o

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c/src/.deps:
.
..
clique.Po
consense.Po
contml.Po
contrast.Po
dnacomp.Po
dnadist.Po
dnainvar.Po
dnaml2.Po
dnamlk2.Po
dnamlk.Po
dnaml.Po
dnapars.Po
dnapenny.Po
dollop.Po
dolpenny.Po
factor.Po
fitch.Po
gendist.Po
kitsch.Po
mix2.Po
mix.Po
neighbor.Po
penny.Po
protdist.Po
protpars.Po
restml2.Po
restml.Po
seqboot.Po

./emboss/EMBOSS-2.5.1/embassy/PHYLIP-3.573c/src/.libs:
.
..
eclique
econsense
econtml
econtrast
ednacomp
ednadist
ednainvar
ednaml
ednamlk
ednapars
ednapenny
edollop
edolpenny
efactor
efitch
egendist
ekitsch
emix
eneighbor
epenny
eprotdist
eprotpars
erestml
eseqboot

./emboss/EMBOSS-2.5.1/embassy/TOPO-0.1:
.
..
aclocal.m4
AUTHORS
ChangeLog
config.log
config.status
configure
configure.in
COPYING
depcomp
emboss_acd
INSTALL
libtool
ltmain.sh
Makefile
Makefile.am
Makefile.in
NEWS
README
source

./emboss/EMBOSS-2.5.1/embassy/TOPO-0.1/emboss_acd:
.
..
codes.english
Makefile
Makefile.am
Makefile.in
topo.acd

./emboss/EMBOSS-2.5.1/embassy/TOPO-0.1/source:
.
..
common.h
.deps
.libs
Makefile
Makefile.am
Makefile.in
topo
topo.c
topo.o

./emboss/EMBOSS-2.5.1/embassy/TOPO-0.1/source/.deps:
.
..
topo.Po

./emboss/EMBOSS-2.5.1/embassy/TOPO-0.1/source/.libs:
.
..
topo

./emboss/EMBOSS-2.5.1/emboss:
.
..
aaindexextract
aaindexextract.c
aaindexextract.o
abiview
abiview.c
abiview.o
acd
acdc
acdc.c
acdc.o
ajtest.c
antigenic
antigenic.c
antigenic.o
backtranseq
backtranseq.c
backtranseq.o
banana
banana.c
banana.o
biosed
biosed.c
biosed.o
btwisted
btwisted.c
btwisted.o
cai
cai.c
cai.o
chaos
chaos.c
chaos.o
charge
charge.c
charge.o
checktrans
checktrans.c
checktrans.o
chips
chips.c
chips.o
cirdna
cirdna.c
cirdna.o
codcmp
codcmp.c
codcmp.o
coderet
coderet.c
coderet.o
complex.c
compseq
compseq.c
compseq.o
cons
cons.c
cons.o
contacts
contacts.c
contacts.o
COPYING
corbatest.c
cpgplot
cpgplot.c
cpgplot.o
cpgreport
cpgreport.c
cpgreport.o
cusp
cusp.c
cusp.o
cutgextract
cutgextract.c
cutgextract.o
cutseq
cutseq.c
cutseq.o
dan
dan.c
dan.o
data
dbiblast
dbiblast.c
dbiblast.o
dbifasta
dbifasta.c
dbifasta.o
dbiflat
dbiflat.c
dbiflat.o
dbigcg
dbigcg.c
dbigcg.o
degapseq
degapseq.c
degapseq.o
demoalign.c
demofeatures.c
demolist.c
demoreport.c
demosequence.c
demostring.c
demotable.c
.deps
descseq
descseq.c
descseq.o
diffseq
diffseq.c
diffseq.o
digest
digest.c
digest.o
distmat
distmat.c
distmat.o
domainer
domainer.c
domainer.o
dotmatcher
dotmatcher.c
dotmatcher.o
dotpath
dotpath.c
dotpath.o
dottup
dottup.c
dottup.o
dreg
dreg.c
dreg.o
einverted
einverted.c
einverted.o
embossdata
embossdata.c
embossdata.o
emboss.default
embossversion
embossversion.c
embossversion.o
emma
emma.c
emma.o
emowse
emowse.c
emowse.o
entrails.c
entret
entret.c
entret.o
eprimer3
eprimer3.c
eprimer3.o
equicktandem
equicktandem.c
equicktandem.o
est2genome
est2genome.c
est2genome.o
etandem
etandem.c
etandem.o
extractfeat
extractfeat.c
extractfeat.o
extractseq
extractseq.c
extractseq.o
findkm
findkm.c
findkm.o
fraggle
fraggle.c
fraggle.o
freak
freak.c
freak.o
funky
funky.c
funky.o
fuzznuc
fuzznuc.c
fuzznuc.o
fuzzpro
fuzzpro.c
fuzzpro.o
fuzztran
fuzztran.c
fuzztran.o
garnier
garnier.c
garnier.o
geecee
geecee.c
geecee.o
getorf
getorf.c
getorf.o
helixturnhelix
helixturnhelix.c
helixturnhelix.o
hetparse
hetparse.c
hetparse.o
histogramtest.c
hmmgen
hmmgen.c
hmmgen.o
hmoment
hmoment.c
hmoment.o
iep
iep.c
iep.o
infoalign
infoalign.c
infoalign.o
infoseq
infoseq.c
infoseq.o
intconv.c
interface
interface.c
interface.o
isochore
isochore.c
isochore.o
jembossctl
jembossctl.c
jembossctl.o
.libs
lindna
lindna.c
lindna.o
listor
listor.c
listor.o
Makefile
Makefile.am
Makefile.in
marscan
marscan.c
marscan.o
maskfeat
maskfeat.c
maskfeat.o
maskseq
maskseq.c
maskseq.o
matcher
matcher.c
matcher.o
megamerger
megamerger.c
megamerger.o
merger
merger.c
merger.o
msbar
msbar.c
msbar.o
mwcontam
mwcontam.c
mwcontam.o
mwfilter
mwfilter.c
mwfilter.o
needle
needle.c
needle.o
newcpgreport
newcpgreport.c
newcpgreport.o
newcpgseek
newcpgseek.c
newcpgseek.o
newseq
newseq.c
newseq.o
noreturn
noreturn.c
noreturn.o
notseq
notseq.c
notseq.o
nthseq
nthseq.c
nthseq.o
octanol
octanol.c
octanol.o
oddcomp
oddcomp.c
oddcomp.o
palindrome
palindrome.c
palindrome.o
pasteseq
pasteseq.c
pasteseq.o
patmatdb
patmatdb.c
patmatdb.o
patmatmotifs
patmatmotifs.c
patmatmotifs.o
patmattest.c
pdbparse
pdbparse.c
pdbparse.o
pdbtosp
pdbtosp.c
pdbtosp.o
pepcoil
pepcoil.c
pepcoil.o
pepinfo
pepinfo.c
pepinfo.o
pepnet
pepnet.c
pepnet.o
pepstats
pepstats.c
pepstats.o
pepwheel
pepwheel.c
pepwheel.o
pepwindow
pepwindowall
pepwindowall.c
pepwindowall.o
pepwindow.c
pepwindow.o
plotcon
plotcon.c
plotcon.o
plotorf
plotorf.c
plotorf.o
polydot
polydot.c
polydot.o
preg
preg.c
preg.o
prettyplot
prettyplot.c
prettyplot.o
prettyseq
prettyseq.c
prettyseq.o
prima.c
primers.c
primersearch
primersearch.c
primersearch.o
printsextract
printsextract.c
printsextract.o
profgen
profgen.c
profgen.o
profit
profit.c
profit.o
prophecy
prophecy.c
prophecy.o
prophet
prophet.c
prophet.o
prosextract
prosextract.c
prosextract.o
pscan
pscan.c
pscan.o
rebaseextract
rebaseextract.c
rebaseextract.o
recoder
recoder.c
recoder.o
redata
redata.c
redata.o
remap
remap.c
remap.o
restover
restover.c
restover.o
restrict
restrict.c
restrict.o
revseq
revseq.c
revseq.o
scopalign
scopalign.c
scopalign.o
scopnr
scopnr.c
scopnr.o
scopparse
scopparse.c
scopparse.o
scoprep
scoprep.c
scoprep.o
scopreso
scopreso.c
scopreso.o
scopseqs
scopseqs.c
scopseqs.o
seealso
seealso.c
seealso.o
seqalign
seqalign.c
seqalign.o
seqinfo.c
seqmatchall
seqmatchall.c
seqmatchall.o
seqnr
seqnr.c
seqnr.o
seqret
seqretall.c
seqretallfeat.c
seqret.c
seqret.o
seqretset.c
seqretsingle.c
seqretsplit
seqretsplit.c
seqretsplit.o
seqsearch
seqsearch.c
seqsearch.o
seqsort
seqsort.c
seqsort.o
seqwords
seqwords.c
seqwords.o
showalign
showalign.c
showalign.o
showdb
showdb.c
showdb.o
showfeat
showfeat.c
showfeat.o
showorf
showorf.c
showorf.o
showseq
showseq.c
showseq.o
shuffleseq
shuffleseq.c
shuffleseq.o
sigcleave
sigcleave.c
sigcleave.o
siggen
siggen.c
siggen.o
sigplot.c
sigscan
sigscan.c
sigscan.o
silent
silent.c
silent.o
skipseq
skipseq.c
skipseq.o
splitter
splitter.c
splitter.o
stretcher
stretcher.c
stretcher.o
stssearch
stssearch.c
stssearch.o
supermatcher
supermatcher.c
supermatcher.o
syco
syco.c
syco.o
testplot.c
textsearch
textsearch.c
textsearch.o
tfextract
tfextract.c
tfextract.o
tfm
tfm.c
tfm.o
tfscan
tfscan.c
tfscan.o
tmap
tmap.c
tmap.o
tranalign
tranalign.c
tranalign.o
transeq
transeq.c
transeq.o
treetypedisplay.c
trimest
trimest.c
trimest.o
trimseq
trimseq.c
trimseq.o
union
union.c
union.o
vectorstrip
vectorstrip.c
vectorstrip.o
water
water.c
water.o
whichdb
whichdb.c
whichdb.o
wobble
wobble.c
wobble.o
wordcount
wordcount.c
wordcount.o
wordmatch
wordmatch.c
wordmatch.o
wossname
wossname.c
wossname.o
yank
yank.c
yank.o

./emboss/EMBOSS-2.5.1/emboss/acd:
.
..
aaindexextract.acd
abiview.acd
ajbad.acd
ajfeatest.acd
ajtest.acd
alignwrap.acd
antigenic.acd
backtranseq.acd
banana.acd
biosed.acd
btwisted.acd
cai.acd
chaos.acd
charge.acd
checktrans.acd
chips.acd
cirdna.acd
codcmp.acd
coderet.acd
codes.english
complex.acd
compseq.acd
cons.acd
contacts.acd
corbatest.acd
cpgplot.acd
cpgreport.acd
cusp.acd
cutgextract.acd
cutseq.acd
dan.acd
dbiblast.acd
dbifasta.acd
dbiflat.acd
dbigcg.acd
degapseq.acd
demoalign.acd
demofeatures.acd
demolist.acd
demoreport.acd
demosequence.acd
demostring.acd
demotable.acd
descseq.acd
dichet.acd
diffseq.acd
digest.acd
distmat.acd
domainer.acd
dotmatcher.acd
dotpath.acd
dottup.acd
dreg.acd
einverted.acd
embossdata.acd
embossversion.acd
emma.acd
emowse.acd
entrails.acd
entret.acd
eprimer3.acd
equicktandem.acd
est2genome.acd
etandem.acd
extractfeat.acd
extractseq.acd
findkm.acd
fraggle.acd
freak.acd
funky.acd
fuzznuc.acd
fuzzpro.acd
fuzztran.acd
garnier.acd
geecee.acd
getorf.acd
helixturnhelix.acd
hetparse.acd
histogramtest.acd
hmmgen.acd
hmoment.acd
iep.acd
infoalign.acd
infoseq.acd
intconv.acd
interface.acd
isochore.acd
lindna.acd
listor.acd
Makefile
Makefile.am
Makefile.in
marscan.acd
maskfeat.acd
maskseq.acd
matcher.acd
megamerger.acd
merger.acd
msbar.acd
mwcontam.acd
mwfilter.acd
needle.acd
newcpgreport.acd
newcpgseek.acd
newseq.acd
noreturn.acd
notseq.acd
nrscope.acd
nthseq.acd
octanol.acd
oddcomp.acd
palindrome.acd
pasteseq.acd
patmatdb.acd
patmatmotifs.acd
patmattest.acd
pdbparse.acd
pdbtosp.acd
pepcoil.acd
pepinfo.acd
pepnet.acd
pepstats.acd
pepwheel.acd
pepwindow.acd
pepwindowall.acd
plotcon.acd
plotorf.acd
polydot.acd
preg.acd
prettyplot.acd
prettyseq.acd
prima.acd
primers.acd
primersearch.acd
printsextract.acd
profgen.acd
profit.acd
prophecy.acd
prophet.acd
prosextract.acd
pscan.acd
psiblasts.acd
qatest.acd
qatestcalcfeat.acd
qatestcalcregexp.acd
qatestcalcseq.acd
qatestcalcseqall.acd
qatestcalcseqset.acd
qatestcalcstring.acd
rebaseextract.acd
recoder.acd
redata.acd
remap.acd
restover.acd
restrict.acd
revseq.acd
scopalign.acd
scope.acd
scopnr.acd
scopparse.acd
scoprep.acd
scopreso.acd
scopseqs.acd
seealso.acd
seqalign.acd
seqinfo.acd
seqmatchall.acd
seqnr.acd
seqret.acd
seqretall.acd
seqretallfeat.acd
seqretset.acd
seqretsingle.acd
seqretsplit.acd
seqsearch.acd
seqsort.acd
seqwords.acd
showalign.acd
showdb.acd
showfeat.acd
showorf.acd
showseq.acd
shuffleseq.acd
sigcleave.acd
siggen.acd
sigplot.acd
sigscan.acd
silent.acd
skipseq.acd
splitter.acd
stretcher.acd
stssearch.acd
supermatcher.acd
swissparse.acd
syco.acd
testplot.acd
textsearch.acd
tfextract.acd
tfm.acd
tfscan.acd
tmap.acd
tranalign.acd
transeq.acd
treetypedisplay.acd
trimest.acd
trimseq.acd
union.acd
vectorstrip.acd
water.acd
whichdb.acd
wobble.acd
wordcount.acd
wordmatch.acd
wossname.acd
yank.acd

./emboss/EMBOSS-2.5.1/emboss/data:
.
..
AAINDEX
CODONS
Eaa_acc_surface.dat
Eaa_hydropathy.dat
Eaa_properties.dat
Eamino.dat
Eangles.dat
Eangles_tri.dat
Eantigenic.dat
Ebases.iub
EBLOSUM30
EBLOSUM35
EBLOSUM40
EBLOSUM45
EBLOSUM50
EBLOSUM55
EBLOSUM60
EBLOSUM62
EBLOSUM62-12
EBLOSUM65
EBLOSUM70
EBLOSUM75
EBLOSUM80
EBLOSUM85
EBLOSUM90
EBLOSUMN
Ecolour.map
Edayhoff.freq
EDNAFULL
EDNAMAT
Edna.melt
Eembl.ior
Eenergy.dat
Efeatures.embl
Efeatures.emboss
Efeatures.gff
Efeatures.pir
Efeatures.protein
Efeatures.swiss
Efreqs.dat
EGC.0
EGC.1
EGC.10
EGC.11
EGC.12
EGC.13
EGC.14
EGC.15
EGC.16
EGC.2
EGC.21
EGC.22
EGC.23
EGC.3
EGC.4
EGC.5
EGC.6
EGC.9
Ehth87.dat
Ehth.dat
Emass.dat
Emassmod.dat
embossre.equ
Ememe.dat
Emwfilter.dat
Enakai.dat
ENUC.4.2
ENUC.4.4
EPAM10
EPAM100
EPAM110
EPAM120
EPAM130
EPAM140
EPAM150
EPAM160
EPAM170
EPAM180
EPAM190
EPAM20
EPAM200
EPAM210
EPAM220
EPAM230
EPAM240
EPAM250
EPAM260
EPAM270
EPAM280
EPAM290
EPAM30
EPAM300
EPAM310
EPAM320
EPAM330
EPAM340
EPAM350
EPAM360
EPAM370
EPAM380
EPAM390
EPAM40
EPAM400
EPAM410
EPAM420
EPAM430
EPAM440
EPAM450
EPAM460
EPAM470
EPAM480
EPAM490
EPAM50
EPAM500
EPAM60
EPAM70
EPAM80
EPAM90
Epepcoil.dat
Epk.dat
Epprofile
Eprior1.plib
Eprior30.plib
Erna.melt
Esig.euk
Esig.pro
Etags.embl
Etags.emboss
Etags.gff
Etags.pir
Etags.protein
Etags.swiss
Evdw.dat
Ewhite-wimley.dat
Makefile
Makefile.am
Makefile.in
nr.Z
PRINTS
PROSITE
REBASE

./emboss/EMBOSS-2.5.1/emboss/data/AAINDEX:
.
..
dummyfile
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/emboss/data/CODONS:
.
..
Eacc.cut
Eadenovirus5.cut
Eadenovirus7.cut
Eaidlav.cut
Eanasp.cut
Eani.cut
Eanidmit.cut
Eani_h.cut
Easn.cut
Eath.cut
Eatu.cut
Eavi.cut
Ebja.cut
Ebly.cut
Ebme.cut
Ebmo.cut
Ebna.cut
Ebov.cut
Ebovsp.cut
Ebst.cut
Ebsu.cut
Ebsu_h.cut
Ecac.cut
Ecal.cut
Eccr.cut
Ecel.cut
Echicken.cut
Echi.cut
Echisp.cut
Echk.cut
Echmp.cut
Echnt.cut
Echos.cut
Echzm.cut
Echzmrubp.cut
Ecpx.cut
Ecre.cut
Ecrisp.cut
Ectr.cut
Edayhoff.cut
Eddi.cut
Eddi_h.cut
Edog.cut
Edro.cut
Edro_h.cut
Edrosophila.cut
Eeca.cut
Eeco.cut
Eeco_h.cut
Eecoli.cut
Ef1.cut
Efish.cut
Efmdvpolyp.cut
Eham.cut
Ehha.cut
Ehin.cut
Ehma.cut
Ehuman.cut
Ehum.cut
Ekla.cut
Ekpn.cut
Ella.cut
Emac.cut
Emaize.cut
Emam_h.cut
Emixlg.cut
Emouse.cut
Emsa.cut
Emse.cut
Emta.cut
Emtu.cut
Emus.cut
Emussp.cut
Emva.cut
Emzecp.cut
Emze.cut
Encr.cut
Eneu.cut
Engo.cut
Eoncsp.cut
Epae.cut
Epea.cut
Epet.cut
Epfa.cut
Ephix174.cut
Ephv.cut
Ephy.cut
Epig.cut
Epolyomaa2.cut
Epombecai.cut
Epombe.cut
Epot.cut
Eppu.cut
Epse.cut
Epsy.cut
Epvu.cut
Erabbit.cut
Erab.cut
Erabsp.cut
Erat.cut
Eratsp.cut
Erca.cut
Erhm.cut
Eric.cut
Erle.cut
Erme.cut
Ersp.cut
Esalsp.cut
Esau.cut
Esco.cut
Esgi.cut
Eshp.cut
Eshpsp.cut
Esli.cut
Eslm.cut
Esma.cut
Esmi.cut
Esmu.cut
Esoy.cut
Espi.cut
Espn.cut
Espo.cut
Espo_h.cut
Espu.cut
Esta.cut
Esty.cut
Esus.cut
Esv40.cut
Esyhsp.cut
Esynsp.cut
Etbr.cut
Etcr.cut
Eter.cut
Etetsp.cut
Etobcp.cut
Etob.cut
Etom.cut
Etrb.cut
Evco.cut
Ewht.cut
Exel.cut
Exenopus.cut
Eyeastcai.cut
Eyeast.cut
Eyen.cut
Eysc.cut
Eysc_h.cut
Eyscmt.cut
Eysp.cut
Ezebrafish.cut
Ezma.cut
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/emboss/data/PRINTS:
.
..
dummyfile
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/emboss/data/PROSITE:
.
..
dummyfile
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/emboss/data/REBASE:
.
..
dummyfile
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/emboss/.deps:
.
..
aaindexextract.Po
abiview.Po
acdc.Po
ajtest.Po
antigenic.Po
backtranseq.Po
banana.Po
biosed.Po
btwisted.Po
cai.Po
chaos.Po
charge.Po
checktrans.Po
chips.Po
cirdna.Po
codcmp.Po
coderet.Po
complex.Po
compseq.Po
cons.Po
contacts.Po
corbatest.Po
cpgplot.Po
cpgreport.Po
cusp.Po
cutgextract.Po
cutseq.Po
dan.Po
dbiblast.Po
dbifasta.Po
dbiflat.Po
dbigcg.Po
degapseq.Po
demoalign.Po
demofeatures.Po
demolist.Po
demoreport.Po
demosequence.Po
demostring.Po
demotable.Po
descseq.Po
diffseq.Po
digest.Po
distmat.Po
domainer.Po
dotmatcher.Po
dotpath.Po
dottup.Po
dreg.Po
einverted.Po
embossdata.Po
embossversion.Po
emma.Po
emowse.Po
entrails.Po
entret.Po
eprimer3.Po
equicktandem.Po
est2genome.Po
etandem.Po
extractfeat.Po
extractseq.Po
findkm.Po
fraggle.Po
freak.Po
funky.Po
fuzznuc.Po
fuzzpro.Po
fuzztran.Po
garnier.Po
geecee.Po
getorf.Po
helixturnhelix.Po
hetparse.Po
histogramtest.Po
hmmgen.Po
hmoment.Po
iep.Po
infoalign.Po
infoseq.Po
intconv.Po
interface.Po
isochore.Po
jembossctl.Po
lindna.Po
listor.Po
marscan.Po
maskfeat.Po
maskseq.Po
matcher.Po
megamerger.Po
merger.Po
msbar.Po
mwcontam.Po
mwfilter.Po
needle.Po
newcpgreport.Po
newcpgseek.Po
newseq.Po
noreturn.Po
notseq.Po
nthseq.Po
octanol.Po
oddcomp.Po
palindrome.Po
pasteseq.Po
patmatdb.Po
patmatmotifs.Po
patmattest.Po
pdbparse.Po
pdbtosp.Po
pepcoil.Po
pepinfo.Po
pepnet.Po
pepstats.Po
pepwheel.Po
pepwindowall.Po
pepwindow.Po
plotcon.Po
plotorf.Po
polydot.Po
preg.Po
prettyplot.Po
prettyseq.Po
prima.Po
primersearch.Po
primers.Po
printsextract.Po
profgen.Po
profit.Po
prophecy.Po
prophet.Po
prosextract.Po
pscan.Po
rebaseextract.Po
recoder.Po
redata.Po
remap.Po
restover.Po
restrict.Po
revseq.Po
scopalign.Po
scopnr.Po
scopparse.Po
scoprep.Po
scopreso.Po
scopseqs.Po
seealso.Po
seqalign.Po
seqinfo.Po
seqmatchall.Po
seqnr.Po
seqretallfeat.Po
seqretall.Po
seqret.Po
seqretset.Po
seqretsingle.Po
seqretsplit.Po
seqsearch.Po
seqsort.Po
seqwords.Po
showalign.Po
showdb.Po
showfeat.Po
showorf.Po
showseq.Po
shuffleseq.Po
sigcleave.Po
siggen.Po
sigplot.Po
sigscan.Po
silent.Po
skipseq.Po
splitter.Po
stretcher.Po
stssearch.Po
supermatcher.Po
syco.Po
testplot.Po
textsearch.Po
tfextract.Po
tfm.Po
tfscan.Po
tmap.Po
tranalign.Po
transeq.Po
treetypedisplay.Po
trimest.Po
trimseq.Po
union.Po
vectorstrip.Po
water.Po
whichdb.Po
wobble.Po
wordcount.Po
wordmatch.Po
wossname.Po
yank.Po

./emboss/EMBOSS-2.5.1/emboss/.libs:
.
..
aaindexextract
abiview
acdc
antigenic
backtranseq
banana
biosed
btwisted
cai
chaos
charge
checktrans
chips
cirdna
codcmp
coderet
compseq
cons
contacts
cpgplot
cpgreport
cusp
cutgextract
cutseq
dan
dbiblast
dbifasta
dbiflat
dbigcg
degapseq
descseq
diffseq
digest
distmat
domainer
dotmatcher
dotpath
dottup
dreg
einverted
embossdata
embossversion
emma
emowse
entret
eprimer3
equicktandem
est2genome
etandem
extractfeat
extractseq
findkm
fraggle
freak
funky
fuzznuc
fuzzpro
fuzztran
garnier
geecee
getorf
helixturnhelix
hetparse
hmmgen
hmoment
iep
infoalign
infoseq
interface
isochore
jembossctl
lindna
listor
lt-embossdata
lt-water
lt-wossname
marscan
maskfeat
maskseq
matcher
megamerger
merger
msbar
mwcontam
mwfilter
needle
newcpgreport
newcpgseek
newseq
noreturn
notseq
nthseq
octanol
oddcomp
palindrome
pasteseq
patmatdb
patmatmotifs
pdbparse
pdbtosp
pepcoil
pepinfo
pepnet
pepstats
pepwheel
pepwindow
pepwindowall
plotcon
plotorf
polydot
preg
prettyplot
prettyseq
primersearch
printsextract
profgen
profit
prophecy
prophet
prosextract
pscan
rebaseextract
recoder
redata
remap
restover
restrict
revseq
scopalign
scopnr
scopparse
scoprep
scopreso
scopseqs
seealso
seqalign
seqmatchall
seqnr
seqret
seqretsplit
seqsearch
seqsort
seqwords
showalign
showdb
showfeat
showorf
showseq
shuffleseq
sigcleave
siggen
sigscan
silent
skipseq
splitter
stretcher
stssearch
supermatcher
syco
textsearch
tfextract
tfm
tfscan
tmap
tranalign
transeq
trimest
trimseq
union
vectorstrip
water
whichdb
wobble
wordcount
wordmatch
wossname
yank

./emboss/EMBOSS-2.5.1/jemboss:
.
..
api
images
lib
LICENSE
Makefile
Makefile.am
Makefile.in
org
README
readme.html
resources
runJemboss.csh
utils

./emboss/EMBOSS-2.5.1/jemboss/api:
.
..
allclasses-frame.html
deprecated-list.html
getClasses.pl
help-doc.html
index-all.html
index.html
makeDocs.csh
Makefile
Makefile.am
Makefile.in
org
overview-tree.html
package-list
packages.html
serialized-form.html
stylesheet.css

./emboss/EMBOSS-2.5.1/jemboss/api/org:
.
..
emboss
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss:
.
..
jemboss
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss:
.
..
gui
Jemboss.html
JembossLogo.html
JembossParams.html
Jemboss.winExit.html
Makefile
Makefile.am
Makefile.in
parser
programs
soap

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/gui:
.
..
AdvancedOptions.html
BuildProgramMenu.html
ColumnData.html
DragJTable.html
filetree
form
LaunchJalView.html
Makefile
Makefile.am
Makefile.in
MemoryComboBox.html
ResultsMenuBar.html
sequenceChooser
SequenceData.html
SequenceList.html
SequenceListTableModel.html
SetUpMenuBar.html
ShowResultSet.html
ShowSavedResults.html
startup
SwingWorker.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/gui/filetree:
.
..
DragTree.html
FileEditorDisplay.html
FileEditorDisplay.PopupListener.html
FileNode.html
FileSave.html
FileSaving.html
Makefile
Makefile.am
Makefile.in
RemoteDragTree.html
RemoteFileNode.html
RemoteFileTreePanel.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/gui/form:
.
..
BuildJembossForm.html
ListFilePanel.html
Makefile
Makefile.am
Makefile.in
MultiLineToolTipUI.html
myComboPopup.html
myComboPopup.myComboUI.html
PlafMacros.html
SectionPanel.html
Separator.html
SetInFileCard.html
SetOutFileCard.html
TextFieldFloat.DecimalNumberDocument.html
TextFieldFloat.html
TextFieldInt.html
TextFieldInt.WholeNumberDocument.html
TextFieldSink.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/gui/sequenceChooser:
.
..
CutNPasteTextArea.html
FileChooser.html
InputSequenceAttributes.html
Makefile
Makefile.am
Makefile.in
OutputSequenceAttributes.html
SequenceFilter.html
TextAreaSink.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/gui/startup:
.
..
Database.html
Makefile
Makefile.am
Makefile.in
ProgList.HorizontalMenu.html
ProgList.html
Splash.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/parser:
.
..
acd
AcdFunResolve.html
AcdVarResolve.html
Ajax.html
Dependent.html
Makefile
Makefile.am
Makefile.in
ParseAcd.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/parser/acd:
.
..
ApplicationFields.html
Application.html
ApplicationParam.html
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/programs:
.
..
JembossProcess.html
ListFile.html
Makefile
Makefile.am
Makefile.in
ResultList.html
RunEmbossApplication.html

./emboss/EMBOSS-2.5.1/jemboss/api/org/emboss/jemboss/soap:
.
..
AuthPopup.html
CallAjax.html
GetWossname.html
JembossRun.html
JembossSoapException.html
Makefile
Makefile.am
Makefile.in
PendingResults.html
PrivateRequest.html
ResListView.html

./emboss/EMBOSS-2.5.1/jemboss/images:
.
..
Backward_arrow_button.gif
Forward_arrow_button.gif
Go_button.gif
Information_button.gif
Jemboss_logo_greyback.gif
Jemboss_logo_large.gif
Jemboss_logo_small.gif
Job_manager_button.gif
Makefile
Makefile.am
Makefile.in
Refresh_button2.gif
Refresh_button.gif

./emboss/EMBOSS-2.5.1/jemboss/lib:
.
..
activation.jar
jakarta-regexp-1.2.jar
jalview.jar
jcert.jar
jnet.jar
jsse.jar
LICENSE.Apache
mail.jar
Makefile
Makefile.am
Makefile.in
README
soap.jar
xerces.jar

./emboss/EMBOSS-2.5.1/jemboss/org:
.
..
emboss
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/jemboss/org/emboss:
.
..
jemboss
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss:
.
..
FileManager.java
gui
JembossJarUtil.java
Jemboss.java
JembossLogo.java
JembossParams.java
Makefile
Makefile.am
Makefile.in
parser
programs
server
soap

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/gui:
.
..
AdvancedOptions.java
Browser.java
BuildProgramMenu.java
filetree
form
LaunchJalView.java
Makefile
Makefile.am
Makefile.in
MemoryComboBox.java
ResultsMenuBar.java
sequenceChooser
SequenceData.java
SequenceList.java
SetUpMenuBar.java
ShowResultSet.java
ShowSavedResults.java
startup
SwingWorker.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/gui/filetree:
.
..
DragTree.java
FileEditorDisplay.java
FileNode.java
FileSave.java
FileSaving.java
LocalAndRemoteFileTreeFrame.java
Makefile
Makefile.am
Makefile.in
RemoteDragTree.java
RemoteFileNode.java
RemoteFileTreePanel.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/gui/form:
.
..
AlignFormat.java
ApplicationNamePanel.java
BuildJembossForm.java
LabelTextBox.java
ListFilePanel.java
Makefile
Makefile.am
Makefile.in
MultiLineToolTipUI.java
myComboPopup.java
PlafMacros.java
ReportFormat.java
SectionPanel.java
Separator.java
SetInFileCard.java
SetOutFileCard.java
TextFieldFloat.java
TextFieldInt.java
TextFieldSink.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/gui/sequenceChooser:
.
..
CutNPasteTextArea.java
FileChooser.java
InputSequenceAttributes.java
Makefile
Makefile.am
Makefile.in
OutputSequenceAttributes.java
SequenceFilter.java
TextAreaSink.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/gui/startup:
.
..
Database.java
Makefile
Makefile.am
Makefile.in
ProgList.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/parser:
.
..
acd
AcdFunResolve.java
AcdVariableResolve.java
AcdVarResolve.java
Ajax.java
AjaxUtil.java
Dependent.java
Makefile
Makefile.am
Makefile.in
ParseAcd.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/parser/acd:
.
..
ApplicationFields.java
Application.java
ApplicationParam.java
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/programs:
.
..
BatchUpdateTimer.java
JembossProcess.java
ListFile.java
Makefile
Makefile.am
Makefile.in
ResultList.java
ResultsUpdateTimer.java
RunEmbossApplication2.java
RunEmbossApplication.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/server:
.
..
JembossAuthServer.java
JembossAuthThread.java
JembossFileAuthServer.java
JembossFileServer.java
JembossServer.java
JembossThread.java
Makefile
Makefile.am
Makefile.in
TestPublicServer.java

./emboss/EMBOSS-2.5.1/jemboss/org/emboss/jemboss/soap:
.
..
AuthPopup.java
CallAjax.java
FileList.java
FileRoots.java
GetACD.java
GetHelp.java
GetWossname.java
JembossRun.java
JembossSoapException.java
Makefile
Makefile.am
Makefile.in
MakeFileSafe.java
PendingResults.java
PrivateRequest.java
PublicRequest.java
ServerSetup.java
ShowDB.java

./emboss/EMBOSS-2.5.1/jemboss/resources:
.
..
filemgr.html
jemboss.properties
Makefile
Makefile.am
Makefile.in
readme.txt
seqList.html
version

./emboss/EMBOSS-2.5.1/jemboss/utils:
.
..
install-jemboss-server.sh
keys.sh
Makefile
Makefile.am
Makefile.in
makeFileManagerJNLP.sh
makeJar.csh
makeJNLP.sh
makeSourceJar.csh
README
template.html

./emboss/EMBOSS-2.5.1/nucleus:
.
..
COPYING
.deps
embaln.c
embaln.h
embaln.lo
embaln.o
embcom.c
embcom.h
embcom.lo
embcom.o
embcons.c
embcons.h
embcons.lo
embcons.o
embdata.c
embdata.h
embdata.lo
embdata.o
embdbi.c
embdbi.h
embdbi.lo
embdbi.o
embest.c
embest.h
embest.lo
embest.o
embexit.c
embexit.h
embexit.lo
embexit.o
embgroup.c
embgroup.h
embgroup.lo
embgroup.o
embiep.c
embiep.h
embiep.lo
embiep.o
embinit.c
embinit.h
embinit.lo
embinit.o
embmat.c
embmat.h
embmat.lo
embmat.o
embmisc.c
embmisc.h
embmisc.lo
embmisc.o
embmol.c
embmol.h
embmol.lo
embmol.o
embnmer.c
embnmer.h
embnmer.lo
embnmer.o
emboss.h
embpat.c
embpat.h
embpat.lo
embpat.o
embprop.c
embprop.h
embprop.lo
embprop.o
embread.c
embread.h
embread.lo
embread.o
embshow.c
embshow.h
embshow.lo
embshow.o
embword.c
embword.h
embword.lo
embword.o
embxyz.c
embxyz.h
embxyz.lo
embxyz.o
libnucleus.la
.libs
Makefile
Makefile.am
Makefile.in

./emboss/EMBOSS-2.5.1/nucleus/.deps:
.
..
embaln.Plo
embcom.Plo
embcons.Plo
embdata.Plo
embdbi.Plo
embest.Plo
embexit.Plo
embgroup.Plo
embiep.Plo
embinit.Plo
embmat.Plo
embmisc.Plo
embmol.Plo
embnmer.Plo
embpat.Plo
embprop.Plo
embread.Plo
embshow.Plo
embword.Plo
embxyz.Plo

./emboss/EMBOSS-2.5.1/nucleus/.libs:
.
..
libnucleus.a
libnucleus.la
libnucleus.lai
libnucleus.so
libnucleus.so.0
libnucleus.so.0.1.0

./emboss/EMBOSS-2.5.1/plplot:
.
..
.deps
dg300.c
dg300.lo
dg300.o
drivers.h
gdpng.c
gdpng.lo
gdpng.o
hpgl.c
hpgl.lo
hpgl.o
impress.c
impress.lo
impress.o
lib
libplplot.la
.libs
linuxvga.c
linuxvga.lo
linuxvga.o
ljii.c
ljii.lo
ljii.o
ljiip.c
ljiip.lo
ljiip.o
Makefile
Makefile.am
Makefile.in
metadefs.h
next.c
next.lo
next.o
null.c
null.lo
null.o
pbm.c
pbm.lo
pbm.o
pdf.h
pdfutils.c
pdfutils.lo
pdfutils.o
plargs.c
plargs.lo
plargs.o
plbox.c
plbox.lo
plbox.o
plbuf.c
plbuf.lo
plbuf.o
plConfig.h
plcont.c
plcont.lo
plcont.o
plcore.c
plcore.h
plcore.lo
plcore.o
plctrl.c
plctrl.lo
plctrl.o
plcvt.c
plcvt.lo
plcvt.o
pldebug.h
plDevs.h
pldtik.c
pldtik.lo
pldtik.o
plevent.h
plfill.c
plfill.lo
plfill.o
plhist.c
plhist.lo
plhist.o
plline.c
plline.lo
plline.o
plmap.c
plmap.lo
plmap.o
plmeta.c
plmeta.lo
plmeta.o
plot3d.c
plot3d.lo
plot3d.o
plpage.c
plpage.lo
plpage.o
plplot.h
plplotP.h
plsdef.c
plsdef.lo
plsdef.o
plshade.c
plshade.lo
plshade.o
plstripc.c
plstripc.lo
plstripc.o
plstrm.h
plsym.c
plsym.lo
plsym.o
pltick.c
pltick.lo
pltick.o
plvpor.c
plvpor.lo
plvpor.o
plwind.c
plwind.lo
plwind.o
plxwd.h
ps.c
ps.lo
ps.o
tek.c
tek.lo
tek.o
xfig.c
xfig.lo
xfig.o
xwin.c
xwin.lo
xwin.o

./emboss/EMBOSS-2.5.1/plplot/.deps:
.
..
dg300.Plo
gdpng.Plo
hpgl.Plo
impress.Plo
linuxvga.Plo
ljii.Plo
ljiip.Plo
next.Plo
null.Plo
pbm.Plo
pdfutils.Plo
plargs.Plo
plbox.Plo
plbuf.Plo
plcont.Plo
plcore.Plo
plctrl.Plo
plcvt.Plo
pldtik.Plo
plfill.Plo
plhist.Plo
plline.Plo
plmap.Plo
plmeta.Plo
plot3d.Plo
plpage.Plo
plsdef.Plo
plshade.Plo
plstripc.Plo
plsym.Plo
pltick.Plo
plvpor.Plo
plwind.Plo
ps.Plo
tek.Plo
xfig.Plo
xwin.Plo

./emboss/EMBOSS-2.5.1/plplot/lib:
.
..
Makefile
Makefile.am
Makefile.in
plstnd5.fnt
plxtnd5.fnt

./emboss/EMBOSS-2.5.1/plplot/.libs:
.
..
libplplot.a
libplplot.la
libplplot.lai
libplplot.so
libplplot.so.5
libplplot.so.5.0.0

./emboss/EMBOSS-2.5.1/scripts:
.
..
autodoc.pl
checkc.pl
cvsscripts
dbilist.pl
dbitest.pl
doctree.pl
edata.i
edata.is
edata.it
edata.out
edithtml.pl
efunc.i
efunc.is
efunc.it
embossdatacheck.pl
embossdatadoc.pl
embossdoccheck.pl
embossdoc.csh
embossdoc.pl
logreport1.pl
makeMake.pl
purify.pl
qatest.pl
README
unused_functions.pl

./emboss/EMBOSS-2.5.1/scripts/cvsscripts:
.
..
automakeembassy
automakeit
makeembassy
makeembassy2
makeemboss
makeemboss2
makeemboss3
makeembosspure

./emboss/EMBOSS-2.5.1/share:
.
..
EMBOSS

./emboss/EMBOSS-2.5.1/share/EMBOSS:
.
..
acd

./emboss/EMBOSS-2.5.1/share/EMBOSS/acd:
.
..
eclique.acd
econsense.acd
econtml.acd
econtrast.acd
ednacomp.acd
ednadist.acd
ednainvar.acd
ednaml.acd
ednamlk.acd
ednapars.acd
ednapenny.acd
edollop.acd
edolpenny.acd
efactor.acd
efitch.acd
egendist.acd
ekitsch.acd
emix.acd
eneighbor.acd
epenny.acd
eprotdist.acd
eprotpars.acd
erestml.acd
eseqboot.acd

./emboss/EMBOSS-2.5.1/test:
.
..
data
embl
.embossrc
gb
genbank
Makefile
Makefile.am
Makefile.in
pir
qa
qatest.dat
swiss
swnew
wormpep

./emboss/EMBOSS-2.5.1/test/data:
.
..
2cmd.con
2cmd.pxyz
2ldx.con
2ldx.pxyz
aaindex1.test
abc.dat
abiview.abi
aligna.dna
alignapart.dna
alignapart.prot
aligna.prot
alignb.dna
alignb.prot
bad.list
cchu.pir
cds.list
cutg.codon
d2cmd_1.con
d2cmd_1.ent
d2cmd_1.pxyz
d2ldx_1.con
d2ldx_1.ent
d2ldx_1.pxyz
data.cirp
data.linp
data.vectorstrip
dna.acedb
dna.aln
dna.asn1
dna.clustal
dna.codata
dna.embl
dna.fasta
dna.fitch
dnagap.fasta
dna.gcg
dna.gcg8
dna.genbank
dna.ig
dna.m-acedb
dna.m-codata
dna.m-embl
dna.m-fasta
dna.m-fasta-long
dna.m-ncbi
dna.msf
dna.msf8
dna.m-strider
dna.ncbi
dna.nonewline
dna.phylip
dna.phylip3
dna.staden
dna.strider
dna.text
emrod
emrod.nhr
emrod.nin
emrod.nsq
enztest.dat
feat.emft
feat.fasta
feat.gbft
feat.pir
featprot.fasta
file1
file2
globins.aln
globins.fasta
globins.gribskov
globins.msf
globins.prophecy
good.list
lac.primers
Lactate_&_malate_dehydrogenases,_N-terminal_domain.align
Makefile
Makefile.am
Makefile.in
mito.seq
molwts.dat
mw1.dat
mw2.dat
mw3.dat
oddcomp.comp
outfile.prophecy
paamir.pep
pax6_cdna.fasta
prev.comp
primers
prints.test
prophecy.gribskov
prosite.dat
prosite.doc
prot.acedb
prot.codata
prot.fasta
prot.gcg
prot.gcg8
prot.ig
prot.m-acedb
prot.m-codata
prot.m-fasta
prot.m-nbrf
prot.m-ncbi
prot.m-swiss
prot.nbrf
prot.ncbi
prot.swiss
prot.text
site.dat
swnew
swnew.phr
swnew.pin
swnew.psq
swsplit
swsplit.00.phr
swsplit.00.pin
swsplit.00.psq
swsplit.01.phr
swsplit.01.pin
swsplit.01.psq
swsplit.02.phr
swsplit.02.pin
swsplit.02.psq
swsplit.03.phr
swsplit.03.pin
swsplit.03.psq
swsplit.04.phr
swsplit.04.pin
swsplit.04.psq
swsplit.pal
test.alignsig
test.findkm
test.hits
testids.fasta
testids.ncbi
test.mowse
test.psihits
test.scopembl
test.scopnr
test.scopraw
test.selex
test.seq
testseqs.ncbi
test.sig
test.sphits
test.terms
tranalign.pep
tranalign.seq
ugly.list
withrefm
wormpep.clone.AB
wormpep.clone.ZK637
z83307.seq

./emboss/EMBOSS-2.5.1/test/embl:
.
..
acnum.hit
acnum.trg
des.hit
des.trg
division.lkp
eem_ba1.ref
eem_ba1.seq
eem_est.ref
eem_est.seq
eem_fun.ref
eem_fun.seq
eem_htginv1.ref
eem_htginv1.seq
eem_hum1.ref
eem_hum1.seq
eem_in.ref
eem_in.seq
eem_ov.ref
eem_ov.seq
eem_ro.ref
eem_ro.seq
eem_vi.ref
eem_vi.seq
entrynam.idx
est.dat
fun.dat
hum1.dat
inv.dat
keyword.hit
keyword.trg
Makefile
Makefile.am
Makefile.in
pln.dat
pro.dat
rod.dat
seqvn.hit
seqvn.trg
sts.dat
taxon.hit
taxon.trg
vrl.dat
vrt.dat

./emboss/EMBOSS-2.5.1/test/gb:
.
..
acnum.hit
acnum.trg
ba.ref
ba.seq
des.hit
des.trg
division.lkp
entrynam.idx
htg.ref
htg.seq
keyword.hit
keyword.trg
Makefile
Makefile.am
Makefile.in
seqvn.hit
seqvn.trg
taxon.hit
taxon.trg

./emboss/EMBOSS-2.5.1/test/genbank:
.
..
acnum.hit
acnum.trg
des.hit
des.trg
division.lkp
entrynam.idx
gbbct1.seq
gbest1.seq
gbinv1.seq
gbpln1.seq
gbpln2.seq
gbpri1.seq
gbrod1.seq
gbsts1.seq
gbvrl1.seq
gbvrt.seq
keyword.hit
keyword.trg
Makefile
Makefile.am
Makefile.in
seqvn.hit
seqvn.trg
taxon.hit
taxon.trg

./emboss/EMBOSS-2.5.1/test/pir:
.
..
acnum.hit
acnum.trg
des.hit
des.trg
division.lkp
entrynam.idx
keyword.hit
keyword.trg
Makefile
Makefile.am
Makefile.in
pir1.header
pir1.names
pir1.numbers
pir1.offset
pir1.ref
pir1.seq
pir2.header
pir2.names
pir2.numbers
pir2.offset
pir2.ref
pir2.seq
pir3.header
pir3.names
pir3.numbers
pir3.offset
pir3.ref
pir3.seq
pir4.header
pir4.names
pir4.numbers
pir4.offset
pir4.ref
pir4.seq
seqvn.hit
seqvn.trg
taxon.hit
taxon.trg

./emboss/EMBOSS-2.5.1/test/qa:
.
..
qatest.csh

./emboss/EMBOSS-2.5.1/test/swiss:
.
..
acnum.hit
acnum.trg
des.hit
des.trg
division.lkp
entrynam.idx
keyword.hit
keyword.trg
Makefile
Makefile.am
Makefile.in
seq.dat
seqvn.hit
seqvn.trg
taxon.hit
taxon.trg

./emboss/EMBOSS-2.5.1/test/swnew:
.
..
acnum.hit
acnum.trg
des.hit
des.trg
division.lkp
entrynam.idx
keyword.hit
keyword.trg
Makefile
Makefile.am
Makefile.in
new_seq.dat
seqvn.hit
seqvn.trg
taxon.hit
taxon.trg
upd_ann.dat
upd_seq.dat

./emboss/EMBOSS-2.5.1/test/wormpep:
.
..
acnum.hit
acnum.trg
des.hit
des.trg
division.lkp
entrynam.idx
Makefile
Makefile.am
Makefile.in
wormpep
wormpep.phr
wormpep.pin
wormpep.psd
wormpep.psi
wormpep.psq

./emboss/EMBOSS-GUI:
.
..
EMBOSS
install.sh

./emboss/EMBOSS-GUI/EMBOSS:
.
..
ACD
GUI

./emboss/EMBOSS-GUI/EMBOSS/ACD:
.
..
ACD.pm
blib
Changes
Makefile
Makefile.PL
MANIFEST
pm_to_blib
README
test.pl

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib:
.
..
arch
lib
man3

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/arch:
.
..
auto

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/arch/auto:
.
..
EMBOSS

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/arch/auto/EMBOSS:
.
..
ACD

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/arch/auto/EMBOSS/ACD:
.
..
.exists

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/lib:
.
..
auto
EMBOSS

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/lib/auto:
.
..
EMBOSS

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/lib/auto/EMBOSS:
.
..
ACD

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/lib/auto/EMBOSS/ACD:
.
..
.exists

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/lib/EMBOSS:
.
..
ACD.pm
.exists

./emboss/EMBOSS-GUI/EMBOSS/ACD/blib/man3:
.
..
EMBOSS::ACD.3pm
.exists

./emboss/EMBOSS-GUI/EMBOSS/GUI:
.
..
blib
Changes
data
GUI.pm
Makefile
Makefile.PL
MANIFEST
pm_to_blib
postamble.pl
README
test.pl

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib:
.
..
arch
lib
man3

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/arch:
.
..
auto

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/arch/auto:
.
..
EMBOSS

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/arch/auto/EMBOSS:
.
..
GUI

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/arch/auto/EMBOSS/GUI:
.
..
.exists

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/lib:
.
..
auto
EMBOSS

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/lib/auto:
.
..
EMBOSS

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/lib/auto/EMBOSS:
.
..
GUI

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/lib/auto/EMBOSS/GUI:
.
..
.exists

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/lib/EMBOSS:
.
..
.exists
GUI.pm
postamble.pl

./emboss/EMBOSS-GUI/EMBOSS/GUI/blib/man3:
.
..
EMBOSS::GUI.3pm
.exists

./emboss/EMBOSS-GUI/EMBOSS/GUI/data:
.
..
email.pl
exclude
html

./emboss/EMBOSS-GUI/EMBOSS/GUI/data/html:
.
..
EMBOSS.css
EMBOSS.js
images
index.html
main.html
runs
title.html

./emboss/EMBOSS-GUI/EMBOSS/GUI/data/html/images:
.
..
back.gif
emboss-title.gif
frame-bottom.gif
frame-helix.gif
go.gif
help.gif
spacer.gif

./emboss/EMBOSS-GUI/EMBOSS/GUI/data/html/runs:
.
..

./emboss/lib:
.
..
libhmmer.a
libhmmer.la
libhmmer.so
libhmmer.so.1
libhmmer.so.1.1.1

./emboss/share:
.
..
EMBOSS

./emboss/share/EMBOSS:
.
..
acd

./emboss/share/EMBOSS/acd:
.
..
ealistat.acd
eclique.acd
econsense.acd
econtml.acd
econtrast.acd
ednacomp.acd
ednadist.acd
ednainvar.acd
ednaml.acd
ednamlk.acd
ednapars.acd
ednapenny.acd
edollop.acd
edolpenny.acd
efactor.acd
efitch.acd
egendist.acd
ehmmalign.acd
ehmmbuild.acd
ehmmcalibrate.acd
ehmmconvert.acd
ehmmemit.acd
ehmmfetch.acd
ehmmindex.acd
ehmmpfam.acd
ehmmsearch.acd
ekitsch.acd
emix.acd
eneighbor.acd
epenny.acd
eprotdist.acd
eprotpars.acd
erestml.acd
eseqboot.acd
topo.acd


