aaindexextract-keep
antigenic-keep
assemblyget-bam2bam-keep
assemblyget-bam2bam2-keep
assemblyget-bamquery2bam-keep
assemblyget-bamquery2bam2-keep

clustalo-test2keep
clustalo-test4keep
clustalo-test9keep
codcopy-outcherry
codcopy-outcodehop
codcopy-outcut
codcopy-outcutg
codcopy-outcutgaa
codcopy-outemboss
codcopy-outgcg
codcopy-outnumstaden
codcopy-outspsum
codcopy-outstaden
codcopy-outtransterm
contacts-keep
contacts-keep2
cutgextract-keep
cutgextract-outfile
cutgextract-species

dbiblast-allnosys-keep
dbiblast-allsys-keep
dbiblast-ex-keep
dbiblast-nosys-keep
dbiblast-split-keep
dbiblast-split-list-keep
dbiblast-split-wild-keep
dbifasta-allnosys-keep
dbifasta-allsys-keep
dbifasta-ex-keep
dbifasta-swiss-keep
dbifasta-worm-keep
dbiflat-embl-allnosys-keep
dbiflat-embl-allsys-keep
dbiflat-ex-keep
dbiflat-genbank-keep
dbiflat-nosys-keep
dbiflat-swiss-keep
dbiflat-swiss-allnosys-keep
dbiflat-swiss-allsys-keep
dbigcg-allnosys-keep
dbigcg-allsys-keep
dbigcg-ex-keep
dbigcg-pir-keep
dbigcg-pirall-keep

dbxedam-keep
dbxfasta-allsys-keep
dbxfasta-ex-keep
dbxfasta-swiss-keep
dbxfasta-worm-keep
dbxflat-all-keep
dbxflat-ex-keep
dbxflat-swiss-keep
dbxgcg-allsys-keep
dbxgcg-ex-keep
dbxgcg-pir-keep
dbxgcg-pirall-keep
dbxobo-keep
dbxresource-keep
dbxtax-keep
dbxuncompress-keep

domainalign-domsearch
domainalign-keep
domainalign-signature
domainer-domainatrix
domainer-keep
domainer-keep2
domainer-signature
domainrep-keep
domainseqs-keep
domainsse-keep

ehmmalign-keep
ehmmbuild-keep
ehmmbuild-keep2
ehmmbuild-keep4
ehmmcalibrate-keep
ehmmcalibrate-keep2
ehmmconvert-keep
ehmmemit-keep
ehmmfetch-keep
ehmmindex-keep
ehmmpfam-keep
ehmmsearch-keep
eiprscan-ex
ememe-keep

intconv-check
jaspextract-keep

ohmmalign-keep
ohmmbuild-keep
ehmmbuild-keep3
ohmmcalibrate-keep
ohmmindex-keep
ohmm-own-keep1
ohmm-own-keep4
ohmm-own2-keep1
ohmm-own2-keep4
ovrnafold-keep

pdbparse-domainatrix
pdbparse-keep
pdbparse-keep2
pdbparse-signature
pdbplus-domainatrix
pdbplus-keep
pdbplus-signature
pdbtosp-domainatrix
pdbtosp-keep
pepstats-keep
printsextract-keep
prosextract-keep

rebaseextract-keep

scopparse-keep
scopparse-signature
scopparse-structure
seqalign-keep
seqfraggle-keep
seqnr-keep
seqsearch-domalign
seqsort-keep
seqsearch-keep
siggen-keep
siggenlig-keep
sites-keep
sites-signature

tfextract-keep

vrnafold-keep

qatest.summary
qatest.cmd
qatest.out
qatest.log
qatest.doclog
