File List

Here is a list of all files with brief descriptions:

README
alnmodel/alignment.cc
alnmodel/alignment.h [code]
alnmodel/alnmodel.cc
alnmodel/qcaln.cc
alnmodel/qcmultialn.cc
alnmodel/README
alnmodel/seqaln2gapos.cpp
alnmodel/variation.cpp
alnview/Alnview.java
alnview/README
automation/loadsatacruz/README
automation/loadtaxonomy/README
automation/loadtaxonomy/SimpleSelect.java
bionj/bionj.cpp
bionj/initialize.cpp
bionj/initialize.h [code]
bionj/ngiden2distance.cpp
bionj/njtree.cpp
bionj/njtree.h [code]
bionj/oldbionj.c
bionj/README
bionj/testbionj.cpp
bioseq/bioseq.cpp
bioseq/bioseq.h [code]
bioseq/codon.cpp
bioseq/codon.h [code]
bioseq/Evolution.h [code]
bioseq/FPGModel.cpp
bioseq/FPGModel.h [code]
bioseq/GModel.h [code]
bioseq/Model.cpp
bioseq/Model.h [code]
bioseq/README
bioseq/testseq.cpp
cadbc/Aceobj.cpp
cadbc/Aceobj.h [code]
cadbc/cadbc.cpp
cadbc/cadbc.h [code]
cadbc/getsubseq.cpp
cadbc/intergenic.cpp
cadbc/Result.cpp
cadbc/Result.h [code]
cadbc/Seqrange.cpp
cadbc/Seqrange.h [code]
cadbc/seqrslt.h [code]
cadbc/testaql.cpp
cadbc/testclt.cpp
cadbc/testobj.cpp
cluster/alnrange.cpp
cluster/alnrange.h [code]
cluster/breakcl.cpp
cluster/ChainAvgrange.cpp
cluster/ChainAvgrange.h [code]
cluster/chimeradetect.cpp
cluster/chimeradetect_mysql.cpp
cluster/clusmethod.cc
cluster/clusmethod.h [code]
cluster/cluster.cc
cluster/cluster.h [code]
cluster/Clusterdump.java
cluster/DBStat.cpp
cluster/DBStat.h [code]
cluster/dumpClusterPrt.java
cluster/dumpClusterTitle.java
cluster/gconst.cpp
cluster/gconst.h [code]
cluster/gecods.cpp
cluster/gecods_mysql.cpp
cluster/group.cpp
cluster/group.h [code]
cluster/hatrees.h [code]
cluster/loadpgdb.cpp
cluster/loadpgdb.h [code]
cluster/orthopara.cc
cluster/picklongrep.cpp
cluster/pickmember.cpp
cluster/pickorthodiv.cpp
cluster/README
cluster/README_group
cluster/rmfalselink.cpp
cluster/scorepair.cpp
cluster/scorepair.h [code]
cluster/subcluster.cpp
cluster/testgsl.cpp
cluster/testread.cpp
cppsocket/ClientSocket.cpp
cppsocket/ClientSocket.h [code]
cppsocket/ServerSocket.cpp
cppsocket/ServerSocket.h [code]
cppsocket/simple_client_main.cpp
cppsocket/simple_server_main.cpp
cppsocket/Socket.cpp
cppsocket/Socket.h [code]
cppsocket/SocketException.h [code]
dbutil/dbinfo.cpp
dbutil/dbinfo.h [code]
dbutil/testdbinfo.cpp
gbprt2ace/gbprt2ace.cpp
genanno/ec/README
genericTree/Aceobj.cpp
genericTree/Aceobj.h [code]
genericTree/Aceobj.java
genericTree/gentree.h [code]
genericTree/README
genericTree/testobj.cpp
genewise/kzgenewise.cpp
graph/fap.cpp
graph/lgraph.cpp
graph/lgraph.h [code]
manageAce/README
md5cpp/driver.cc
md5cpp/md5.cc
md5cpp/md5.h [code]
md5cpp/README
md5cpp/testmd5.cpp
ortho/CDSload.java
ortho/DumpCDSLoadFile.java
ortho/LoadCDSFromAce.java
ortho/LoadCDSFromOneDB.java
ortho/Orgload.java
ortho/README
ortho/TestAcedb.java
parsetree/gentree.cpp
parsetree/gentree.h [code]
parsetree/gpcrtree.cpp
pirtoace/check.cpp
pirtoace/date.cpp
pirtoace/date.h [code]
pirtoace/head.cpp
pirtoace/head.h [code]
pirtoace/parerr.cpp
pirtoace/parerr.h [code]
pirtoace/pir2ace.cpp
pirtoace/strformat.cpp
pirtoace/strformat.h [code]
range/checkchimera.cpp
range/combest.cpp
range/Esambl.cpp
range/Esambl.h [code]
range/ESTCombined.cpp
range/ESTCombined.h [code]
range/GenModel.cpp
range/GenModel.h [code]
range/Gmapres.cpp
range/Gmapres.h [code]
range/Interval.cpp
range/Interval.h [code]
range/nrep.cpp
range/Range.cpp
range/Range.h [code]
range/README
range/README.nrep
range/RNAModel.cpp
range/RNAModel.h [code]
range/testEsambl.cpp
range/testExon.cpp
range/testGModel.cpp
range/testinterval.cpp
range/TranscriptExon.cpp
range/TranscriptExon.h [code]
seqaln/randist/expdist.c
seqaln/randist/genigfsr.c
seqaln/randist/GFSR.c
seqaln/randist/GFSR.h [code]
seqaln/randist/normdist.c
seqaln/randist/unidist.c
seqaln/seqaln/demo/i_fitD.c
seqaln/seqaln/demo/i_fitS.c
seqaln/seqaln/demo/i_globalD.c
seqaln/seqaln/demo/i_globalS.c
seqaln/seqaln/demo/i_localS.c
seqaln/seqaln/demo/i_mfitD.c
seqaln/seqaln/demo/i_mfitS.c
seqaln/seqaln/demo/i_mglobalD.c
seqaln/seqaln/demo/i_mglobalS.c
seqaln/seqaln/demo/i_mlocalS.c
seqaln/seqaln/demo/i_moverS.c
seqaln/seqaln/demo/i_mpvlocalS.c
seqaln/seqaln/demo/i_mpvsrlocalS.c
seqaln/seqaln/demo/i_msrlocalS.c
seqaln/seqaln/demo/i_mtrlocalS.c
seqaln/seqaln/demo/i_overS.c
seqaln/seqaln/demo/i_pfitS.c
seqaln/seqaln/demo/i_pvlocalS.c
seqaln/seqaln/demo/i_pvsrlocalS.c
seqaln/seqaln/demo/i_srlocalS.c
seqaln/seqaln/demo/i_trlocalS.c
seqaln/seqaln/demo/mlocalSDB.c
seqaln/seqaln/doc/man/icat.c
seqaln/seqaln/doc/man/README
seqaln/seqaln/kzaln/aln.cpp
seqaln/seqaln/kzaln/aln.h [code]
seqaln/seqaln/kzaln/aln_input.h [code]
seqaln/seqaln/kzaln/aln_output.h [code]
seqaln/seqaln/kzaln/alnfn.h [code]
seqaln/seqaln/kzaln/dynamicaln.h [code]
seqaln/seqaln/kzaln/helper.h [code]
seqaln/seqaln/kzaln/i_globalS.c
seqaln/seqaln/kzaln/mgaln.h [code]
seqaln/seqaln/kzaln/mgsaln.cpp
seqaln/seqaln/kzaln/mlocalS_str.cpp
seqaln/seqaln/kzaln/mlocalS_str.h [code]
seqaln/seqaln/kzaln/mlocalSDB.cpp
seqaln/seqaln/kzaln/README
seqaln/seqaln/kzaln/seqaln.h [code]
seqaln/seqaln/kzaln/tabaln.cpp
seqaln/seqaln/kzaln/tabaln_same.cpp
seqaln/seqaln/kzaln/testaln.cpp
seqaln/seqaln/kzaln/util.h [code]
seqaln/seqaln/src/a.h [code]
seqaln/seqaln/src/aln_input.c
seqaln/seqaln/src/aln_input.h [code]
seqaln/seqaln/src/aln_output.c
seqaln/seqaln/src/aln_output.h [code]
seqaln/seqaln/src/alnfn.h [code]
seqaln/seqaln/src/bestincol.c
seqaln/seqaln/src/bestinrow.c
seqaln/seqaln/src/dynamicaln.h [code]
seqaln/seqaln/src/fddeclump.c
seqaln/seqaln/src/fitD.c
seqaln/seqaln/src/fitS.c
seqaln/seqaln/src/fsdeclump.c
seqaln/seqaln/src/gen_align.c
seqaln/seqaln/src/getbest.c
seqaln/seqaln/src/getpvalue.c
seqaln/seqaln/src/globalD.c
seqaln/seqaln/src/globalS.c
seqaln/seqaln/src/helper.c
seqaln/seqaln/src/helper.h [code]
seqaln/seqaln/src/linreg.c
seqaln/seqaln/src/localS.c
seqaln/seqaln/src/ls20.c
seqaln/seqaln/src/lsdeclump.c
seqaln/seqaln/src/make_seq.c
seqaln/seqaln/src/markdiag.c
seqaln/seqaln/src/markseq.c
seqaln/seqaln/src/mccaldon.h [code]
seqaln/seqaln/src/nextpval.c
seqaln/seqaln/src/overS.c
seqaln/seqaln/src/pfitS.c
seqaln/seqaln/src/pfsdeclump.c
seqaln/seqaln/src/prpt_row.c
seqaln/seqaln/src/ptrace.c
seqaln/seqaln/src/pvlocalS.c
seqaln/seqaln/src/pvsrlocalS.c
seqaln/seqaln/src/results_init.c
seqaln/seqaln/src/seqaln.h [code]
seqaln/seqaln/src/srlocalS.c
seqaln/seqaln/src/srlsdeclump.c
seqaln/seqaln/src/topscore.c
seqaln/seqaln/src/trace.c
seqaln/seqaln/src/trlocalS.c
seqaln/seqaln/src/trlsdeclump.c
seqaln/seqaln/src/trrpt_alignment.c
seqaln/seqaln/src/trrpt_scores.c
seqaln/seqaln/src/trtrace.c
seqaln/seqaln/src/util.c
seqaln/seqaln/src/util.h [code]
seqaln/seqaln/util/pir_to_fasta.c
seqaln/src/alnparam.h [code]
seqaln/src/chaining.cpp
seqaln/src/dbaln.cpp
seqaln/src/dbaln_cds.cpp
seqaln/src/dbaln_chimera.cpp
seqaln/src/dbaln_chimerarmsimp.cpp
seqaln/src/dbaln_chimerathread.cpp
seqaln/src/dbaln_fungal.cpp
seqaln/src/dbaln_fungalbt.cpp
seqaln/src/dbaln_fungalrmsimp.cpp
seqaln/src/dbaln_nr.cpp
seqaln/src/dbalnhelper.cpp
seqaln/src/dbalnhelper.h [code]
seqaln/src/DBInfo.cpp
seqaln/src/DBInfo.h [code]
seqaln/src/dynaln.cpp
seqaln/src/dynaln.h [code]
seqaln/src/gwseedaln.cpp
seqaln/src/helper.h [code]
seqaln/src/matrix.cpp
seqaln/src/matrix.h [code]
seqaln/src/README
seqaln/src/testaln.cpp
seqaln/src/testDBInfo.cpp
seqaln/src/testmatrix.cpp
seqaln/src/testmysql.cpp
seqaln/src/blast/alignseg.cpp
seqaln/src/blast/alignseg.h [code]
seqaln/src/blast/boxchain.cpp
seqaln/src/blast/boxchain.h [code]
seqaln/src/blast/kzblast.cpp
seqaln/src/blast/kzblast.h [code]
seqaln/src/blast/linktrie.cpp
seqaln/src/blast/linktrie.h [code]
seqaln/src/blast/README
seqaln/src/blast/testblast.cpp
seqaln/Utility/addentropy.cpp
seqaln/Utility/Blmodel.cpp
seqaln/Utility/Blmodel.h [code]
seqaln/Utility/buildjgitranscript.cpp
seqaln/Utility/buildlocusinfo.cpp
seqaln/Utility/compnr2gentropy.cpp
seqaln/Utility/computenrEntropy.cpp
seqaln/Utility/dumpcds.cpp
seqaln/Utility/footprintHelper.cpp
seqaln/Utility/footprintHelper.h [code]
seqaln/Utility/GeneModel.h [code]
seqaln/Utility/Match.cpp
seqaln/Utility/Match.h [code]
seqaln/Utility/mergefootprint.cpp
seqaln/Utility/Mysqlhelper.h [code]
seqaln/Utility/pfog.cpp
seqaln/Utility/pfogfile.cpp
seqaln/Utility/pfogmultipledb.cpp
seqaln/Utility/pickrepmodel.cpp
seqaln/Utility/picktopcds.cpp
seqaln/Utility/picktopfootprint.cpp
seqaln/Utility/picktopmodel.cpp
seqaln/Utility/preparegw.cpp
seqaln/Utility/README
seqaln/Utility/rmsimpmatch.cpp
seqaln/Utility/seqhelper.cpp
seqaln/Utility/seqhelper.h [code]
seqaln/Utility/simple.cpp
seqaln/Utility/Tblastnmy.h [code]
seqaln/Utility/testrange.cpp
seqaln/Utility/testsimple.cpp
seqaln/Utility/testsys.cpp
seqaln/Utility/wolm.cpp
seqana/Altranscript.java
seqana/blast.cpp
seqana/blast.h [code]
seqana/blpur.cpp
seqana/blpurify.cpp
seqana/ExtractEnd.java
seqana/match.cpp
seqana/match.h [code]
seqana/matrix.h [code]
seqana/ModmRNAvalidate.java
seqana/MSPcrunch.h [code]
seqana/prtMatrix.h [code]
seqana/README
seqana/Region.java
seqana/RegionInt.java
seqana/RegionStr.java
seqana/selortho.cpp
seqana/blastio/blast.cpp
seqana/blastio/blast.h [code]
seqana/blastio/blpur.cpp
seqana/blastio/blpurify.cpp
seqana/blastio/filterblast.cpp
seqana/blastio/match.cpp
seqana/blastio/match.h [code]
seqana/blastio/matrix.h [code]
seqana/blastio/MSPcrunch.h [code]
seqana/blastio/prtMatrix.h [code]
seqana/blastio/README
seqana/blastio/selortho.cpp
seqana/filternr/README
seqana/filternr/WeatherWizard.java
seqana/runsgeblast/README
seqana/seqsep/estsep.cpp
seqana/seqsep/nameoutfile.cpp
seqana/seqsep/nameoutfile.h [code]
seqana/seqsep/picknewseq.cpp
seqana/seqsep/README
seqana/seqsep/rmfrgss.cpp
seqana/seqsep/seqdiv.cpp
seqana/seqsep/seqsep.cpp
seqana/seqsep/version.cpp
seqana/seqsep/version.h [code]
seqconv/README
seqconv/gbtoace/check.cpp
seqconv/gbtoace/date.cpp
seqconv/gbtoace/date.h [code]
seqconv/gbtoace/dseq.cpp
seqconv/gbtoace/dseq.h [code]
seqconv/gbtoace/feature.cpp
seqconv/gbtoace/feature.h [code]
seqconv/gbtoace/featureError.cpp
seqconv/gbtoace/featureError.h [code]
seqconv/gbtoace/fqtable.h [code]
seqconv/gbtoace/g2a.cpp
seqconv/gbtoace/gb2ace.cpp
seqconv/gbtoace/gberr.cpp
seqconv/gbtoace/gberr.h [code]
seqconv/gbtoace/gbfn.cpp
seqconv/gbtoace/gbfn.h [code]
seqconv/gbtoace/gbseq.cpp
seqconv/gbtoace/gbseq.h [code]
seqconv/gbtoace/gdna2a.cpp
seqconv/gbtoace/gprt2a.cpp
seqconv/gbtoace/head.cpp
seqconv/gbtoace/head.h [code]
seqconv/gbtoace/pfeature.cpp
seqconv/gbtoace/pfeature.h [code]
seqconv/gbtoace/README
seqconv/gbtoace/ref.cpp
seqconv/gbtoace/ref.h [code]
seqconv/gbtoace/Reference.cpp
seqconv/gbtoace/reference.h [code]
seqconv/gbtoace/Reference.h [code]
seqconv/gbtoace/Refreader.cpp
seqconv/gbtoace/Refreader.h [code]
seqconv/gbtoace/seqinfo.cpp
seqconv/gbtoace/seqinfo.h [code]
seqconv/gbtoace/test.cpp
seqconv/gbtoace/vref.cpp
seqconv/gbtoace/vref.h [code]
seqconv/sptoace/book.cpp
seqconv/sptoace/book.h [code]
seqconv/sptoace/dbtime.cpp
seqconv/sptoace/dbtime.h [code]
seqconv/sptoace/parsererror.h [code]
seqconv/sptoace/parsesw.cpp
seqconv/sptoace/prt.cpp
seqconv/sptoace/prt.h [code]
seqconv/sptoace/refloc.cpp
seqconv/sptoace/refloc.h [code]
seqconv/sptoace/test.cpp
seqconv/sptoace/time.cpp
seqconv/sptoace/time.h [code]
seqconv/sptoace/util.cpp
seqconv/sptoace/util.h [code]
sim4cpp/align.cpp
sim4cpp/align.h [code]
sim4cpp/args.cpp
sim4cpp/args.h [code]
sim4cpp/dbformat.cpp
sim4cpp/discrim.cpp
sim4cpp/discrim.h [code]
sim4cpp/dna.cpp
sim4cpp/dna.h [code]
sim4cpp/encoding.cpp
sim4cpp/encoding.h [code]
sim4cpp/kzseq.cpp
sim4cpp/kzseq.h [code]
sim4cpp/libc.h [code]
sim4cpp/misc.cpp
sim4cpp/misc.h [code]
sim4cpp/prnt.cpp
sim4cpp/prnt.h [code]
sim4cpp/psublast.h [code]
sim4cpp/sim4.cpp
sim4cpp/sim4.h [code]
sim4cpp/sim4b1.cpp
sim4cpp/sim4b1.h [code]
sim4cpp/sim4main.cpp
sim4cpp/splice.cpp
sim4cpp/splice.h [code]
sim4cpp/strformat.cpp
sim4cpp/strformat.h [code]
sim4cpp/types.h [code]
sim4cpp/Xtend1.cpp
sim4cpp/Xtend1.h [code]
util/codon.h [code]
util/dbinfo.cpp
util/dbinfo.h [code]
util/dynaln.h [code]
util/FPGModel.h [code]
util/GModel.h [code]
util/GrishinDistance.cpp
util/matrix.h [code]
util/Model.h [code]
util/stddev.h [code]
util/strformat.cpp
util/strformat.h [code]
util/test.cpp
util/testlib.cpp
web/README
web/README.ticket
web/cgi/phpinfo.php
web/ec/README
web/jobsearch/README