AUTHORS
Bio/Factory/EMBOSS.pm
Bio/Tools/Run/Alignment/Blat.pm
Bio/Tools/Run/Alignment/Clustalw.pm
Bio/Tools/Run/Alignment/DBA.pm
Bio/Tools/Run/Alignment/Lagan.pm
Bio/Tools/Run/Alignment/Sim4.pm
Bio/Tools/Run/Alignment/StandAloneFasta.pm
Bio/Tools/Run/Alignment/TCoffee.pm
Bio/Tools/Run/Analysis.pm
Bio/Tools/Run/Analysis/soap.pm
Bio/Tools/Run/AnalysisFactory.pm
Bio/Tools/Run/AnalysisFactory/Pise.pm
Bio/Tools/Run/AnalysisFactory/soap.pm
Bio/Tools/Run/Coil.pm
Bio/Tools/Run/EMBOSSacd.pm
Bio/Tools/Run/EMBOSSApplication.pm
Bio/Tools/Run/Eponine.pm
Bio/Tools/Run/FootPrinter.pm
Bio/Tools/Run/Genewise.pm
Bio/Tools/Run/Genscan.pm
Bio/Tools/Run/Hmmer.pm
Bio/Tools/Run/Hmmpfam.pm
Bio/Tools/Run/Mdust.pm
Bio/Tools/Run/Phylo/Molphy/ProtML.pm
Bio/Tools/Run/Phylo/PAML/Codeml.pm
Bio/Tools/Run/Phylo/PAML/Yn00.pm
Bio/Tools/Run/Phylo/Phylip/Base.pm
Bio/Tools/Run/Phylo/Phylip/Consense.pm
Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
Bio/Tools/Run/PiseApplication.pm
Bio/Tools/Run/PiseApplication/abiview.pm
Bio/Tools/Run/PiseApplication/addquart.pm
Bio/Tools/Run/PiseApplication/align2model.pm
Bio/Tools/Run/PiseApplication/alistat.pm
Bio/Tools/Run/PiseApplication/antigenic.pm
Bio/Tools/Run/PiseApplication/assp.pm
Bio/Tools/Run/PiseApplication/backtranseq.pm
Bio/Tools/Run/PiseApplication/bambe.pm
Bio/Tools/Run/PiseApplication/banana.pm
Bio/Tools/Run/PiseApplication/bionj.pm
Bio/Tools/Run/PiseApplication/biosed.pm
Bio/Tools/Run/PiseApplication/bl2seq.pm
Bio/Tools/Run/PiseApplication/blast2.pm
Bio/Tools/Run/PiseApplication/blimps.pm
Bio/Tools/Run/PiseApplication/blimps_block.pm
Bio/Tools/Run/PiseApplication/blimps_matrix.pm
Bio/Tools/Run/PiseApplication/boxshade.pm
Bio/Tools/Run/PiseApplication/btwisted.pm
Bio/Tools/Run/PiseApplication/cai.pm
Bio/Tools/Run/PiseApplication/cap.pm
Bio/Tools/Run/PiseApplication/cds.pm
Bio/Tools/Run/PiseApplication/chaos.pm
Bio/Tools/Run/PiseApplication/charge.pm
Bio/Tools/Run/PiseApplication/checktrans.pm
Bio/Tools/Run/PiseApplication/chips.pm
Bio/Tools/Run/PiseApplication/cirdna.pm
Bio/Tools/Run/PiseApplication/clique.pm
Bio/Tools/Run/PiseApplication/clustalw.pm
Bio/Tools/Run/PiseApplication/clustalw_convert.pm
Bio/Tools/Run/PiseApplication/codcmp.pm
Bio/Tools/Run/PiseApplication/coderet.pm
Bio/Tools/Run/PiseApplication/codnocod.pm
Bio/Tools/Run/PiseApplication/codontree.pm
Bio/Tools/Run/PiseApplication/codonw.pm
Bio/Tools/Run/PiseApplication/comalign.pm
Bio/Tools/Run/PiseApplication/combat.pm
Bio/Tools/Run/PiseApplication/compseq.pm
Bio/Tools/Run/PiseApplication/con_filter.pm
Bio/Tools/Run/PiseApplication/confmat.pm
Bio/Tools/Run/PiseApplication/cons.pm
Bio/Tools/Run/PiseApplication/consense.pm
Bio/Tools/Run/PiseApplication/consensus.pm
Bio/Tools/Run/PiseApplication/cpgplot.pm
Bio/Tools/Run/PiseApplication/cpgreport.pm
Bio/Tools/Run/PiseApplication/CSR.pm
Bio/Tools/Run/PiseApplication/cusp.pm
Bio/Tools/Run/PiseApplication/cutseq.pm
Bio/Tools/Run/PiseApplication/dan.pm
Bio/Tools/Run/PiseApplication/dca.pm
Bio/Tools/Run/PiseApplication/decorate.pm
Bio/Tools/Run/PiseApplication/degapseq.pm
Bio/Tools/Run/PiseApplication/descseq.pm
Bio/Tools/Run/PiseApplication/dialign2.pm
Bio/Tools/Run/PiseApplication/diffseq.pm
Bio/Tools/Run/PiseApplication/digest.pm
Bio/Tools/Run/PiseApplication/distmat.pm
Bio/Tools/Run/PiseApplication/distquart.pm
Bio/Tools/Run/PiseApplication/dnadist.pm
Bio/Tools/Run/PiseApplication/dnapars.pm
Bio/Tools/Run/PiseApplication/dollop.pm
Bio/Tools/Run/PiseApplication/domainer.pm
Bio/Tools/Run/PiseApplication/dotmatcher.pm
Bio/Tools/Run/PiseApplication/dotpath.pm
Bio/Tools/Run/PiseApplication/dottup.pm
Bio/Tools/Run/PiseApplication/drawgram.pm
Bio/Tools/Run/PiseApplication/drawpyr.pm
Bio/Tools/Run/PiseApplication/drawtree.pm
Bio/Tools/Run/PiseApplication/dreg.pm
Bio/Tools/Run/PiseApplication/druid.pm
Bio/Tools/Run/PiseApplication/dsc.pm
Bio/Tools/Run/PiseApplication/dssp.pm
Bio/Tools/Run/PiseApplication/einverted.pm
Bio/Tools/Run/PiseApplication/emma.pm
Bio/Tools/Run/PiseApplication/emowse.pm
Bio/Tools/Run/PiseApplication/environ.pm
Bio/Tools/Run/PiseApplication/eprimer3.pm
Bio/Tools/Run/PiseApplication/equicktandem.pm
Bio/Tools/Run/PiseApplication/est2genome.pm
Bio/Tools/Run/PiseApplication/etandem.pm
Bio/Tools/Run/PiseApplication/extractfeat.pm
Bio/Tools/Run/PiseApplication/extractseq.pm
Bio/Tools/Run/PiseApplication/fasta.pm
Bio/Tools/Run/PiseApplication/fastdnaml.pm
Bio/Tools/Run/PiseApplication/fastrna.pm
Bio/Tools/Run/PiseApplication/filtersites.pm
Bio/Tools/Run/PiseApplication/findkm.pm
Bio/Tools/Run/PiseApplication/fitch.pm
Bio/Tools/Run/PiseApplication/fmtseq.pm
Bio/Tools/Run/PiseApplication/freak.pm
Bio/Tools/Run/PiseApplication/fuzznuc.pm
Bio/Tools/Run/PiseApplication/fuzzpro.pm
Bio/Tools/Run/PiseApplication/fuzztran.pm
Bio/Tools/Run/PiseApplication/gb2xml.pm
Bio/Tools/Run/PiseApplication/geecee.pm
Bio/Tools/Run/PiseApplication/genscan.pm
Bio/Tools/Run/PiseApplication/getblock.pm
Bio/Tools/Run/PiseApplication/getorf.pm
Bio/Tools/Run/PiseApplication/gff2ps.pm
Bio/Tools/Run/PiseApplication/gibbs.pm
Bio/Tools/Run/PiseApplication/gibbs_scan.pm
Bio/Tools/Run/PiseApplication/golden.pm
Bio/Tools/Run/PiseApplication/grailclnt.pm
Bio/Tools/Run/PiseApplication/gruppi.pm
Bio/Tools/Run/PiseApplication/helixturnhelix.pm
Bio/Tools/Run/PiseApplication/hmmalign.pm
Bio/Tools/Run/PiseApplication/hmmbuild.pm
Bio/Tools/Run/PiseApplication/hmmcalibrate.pm
Bio/Tools/Run/PiseApplication/hmmconvert.pm
Bio/Tools/Run/PiseApplication/hmmemit.pm
Bio/Tools/Run/PiseApplication/hmmer2sam.pm
Bio/Tools/Run/PiseApplication/hmmfetch.pm
Bio/Tools/Run/PiseApplication/hmmpfam.pm
Bio/Tools/Run/PiseApplication/hmmscore.pm
Bio/Tools/Run/PiseApplication/hmmsearch.pm
Bio/Tools/Run/PiseApplication/hmoment.pm
Bio/Tools/Run/PiseApplication/homology.pm
Bio/Tools/Run/PiseApplication/html4blast.pm
Bio/Tools/Run/PiseApplication/iep.pm
Bio/Tools/Run/PiseApplication/infoalign.pm
Bio/Tools/Run/PiseApplication/infoseq.pm
Bio/Tools/Run/PiseApplication/interface.pm
Bio/Tools/Run/PiseApplication/isochore.pm
Bio/Tools/Run/PiseApplication/kitsch.pm
Bio/Tools/Run/PiseApplication/lassap.pm
Bio/Tools/Run/PiseApplication/lgicsearch.pm
Bio/Tools/Run/PiseApplication/lindna.pm
Bio/Tools/Run/PiseApplication/listor.pm
Bio/Tools/Run/PiseApplication/loadseq.pm
Bio/Tools/Run/PiseApplication/lvb.pm
Bio/Tools/Run/PiseApplication/makehist.pm
Bio/Tools/Run/PiseApplication/map.pm
Bio/Tools/Run/PiseApplication/marscan.pm
Bio/Tools/Run/PiseApplication/maskfeat.pm
Bio/Tools/Run/PiseApplication/maskseq.pm
Bio/Tools/Run/PiseApplication/matcher.pm
Bio/Tools/Run/PiseApplication/megamerger.pm
Bio/Tools/Run/PiseApplication/melting.pm
Bio/Tools/Run/PiseApplication/merger.pm
Bio/Tools/Run/PiseApplication/mfold.pm
Bio/Tools/Run/PiseApplication/mix.pm
Bio/Tools/Run/PiseApplication/modelfromalign.pm
Bio/Tools/Run/PiseApplication/most.pm
Bio/Tools/Run/PiseApplication/mreps.pm
Bio/Tools/Run/PiseApplication/msa.pm
Bio/Tools/Run/PiseApplication/msbar.pm
Bio/Tools/Run/PiseApplication/mspcrunch.pm
Bio/Tools/Run/PiseApplication/mview_alig.pm
Bio/Tools/Run/PiseApplication/mview_blast.pm
Bio/Tools/Run/PiseApplication/mwfilter.pm
Bio/Tools/Run/PiseApplication/needle.pm
Bio/Tools/Run/PiseApplication/neighbor.pm
Bio/Tools/Run/PiseApplication/newcpgreport.pm
Bio/Tools/Run/PiseApplication/newcpgseek.pm
Bio/Tools/Run/PiseApplication/newseq.pm
Bio/Tools/Run/PiseApplication/njdist.pm
Bio/Tools/Run/PiseApplication/nnssp.pm
Bio/Tools/Run/PiseApplication/notseq.pm
Bio/Tools/Run/PiseApplication/nrscope.pm
Bio/Tools/Run/PiseApplication/nthseq.pm
Bio/Tools/Run/PiseApplication/octanol.pm
Bio/Tools/Run/PiseApplication/oddcomp.pm
Bio/Tools/Run/PiseApplication/palindrome.pm
Bio/Tools/Run/PiseApplication/pam.pm
Bio/Tools/Run/PiseApplication/parciquart.pm
Bio/Tools/Run/PiseApplication/pars.pm
Bio/Tools/Run/PiseApplication/pasteseq.pm
Bio/Tools/Run/PiseApplication/patmatdb.pm
Bio/Tools/Run/PiseApplication/patmatmotifs.pm
Bio/Tools/Run/PiseApplication/patser.pm
Bio/Tools/Run/PiseApplication/pdbsearch.pm
Bio/Tools/Run/PiseApplication/pepcoil.pm
Bio/Tools/Run/PiseApplication/pepinfo.pm
Bio/Tools/Run/PiseApplication/pepnet.pm
Bio/Tools/Run/PiseApplication/pepstats.pm
Bio/Tools/Run/PiseApplication/pepwheel.pm
Bio/Tools/Run/PiseApplication/pepwindow.pm
Bio/Tools/Run/PiseApplication/pepwindowall.pm
Bio/Tools/Run/PiseApplication/pestfind.pm
Bio/Tools/Run/PiseApplication/pftools.pm
Bio/Tools/Run/PiseApplication/phiblast.pm
Bio/Tools/Run/PiseApplication/pima.pm
Bio/Tools/Run/PiseApplication/plotcon.pm
Bio/Tools/Run/PiseApplication/plotorf.pm
Bio/Tools/Run/PiseApplication/plsearch.pm
Bio/Tools/Run/PiseApplication/polydot.pm
Bio/Tools/Run/PiseApplication/pratt.pm
Bio/Tools/Run/PiseApplication/predator.pm
Bio/Tools/Run/PiseApplication/preg.pm
Bio/Tools/Run/PiseApplication/prettyalign.pm
Bio/Tools/Run/PiseApplication/prettyplot.pm
Bio/Tools/Run/PiseApplication/prettyseq.pm
Bio/Tools/Run/PiseApplication/primersearch.pm
Bio/Tools/Run/PiseApplication/primo.pm
Bio/Tools/Run/PiseApplication/prodom.pm
Bio/Tools/Run/PiseApplication/profit.pm
Bio/Tools/Run/PiseApplication/prophecy.pm
Bio/Tools/Run/PiseApplication/prophet.pm
Bio/Tools/Run/PiseApplication/prose.pm
Bio/Tools/Run/PiseApplication/prot_nucml.pm
Bio/Tools/Run/PiseApplication/protal2dna.pm
Bio/Tools/Run/PiseApplication/protdist.pm
Bio/Tools/Run/PiseApplication/protpars.pm
Bio/Tools/Run/PiseApplication/pscan.pm
Bio/Tools/Run/PiseApplication/psiblast.pm
Bio/Tools/Run/PiseApplication/psort2.pm
Bio/Tools/Run/PiseApplication/Puzzle.pm
Bio/Tools/Run/PiseApplication/pyramids.pm
Bio/Tools/Run/PiseApplication/pyreval.pm
Bio/Tools/Run/PiseApplication/qstar.pm
Bio/Tools/Run/PiseApplication/quicktree.pm
Bio/Tools/Run/PiseApplication/readnexus.pm
Bio/Tools/Run/PiseApplication/readseq.pm
Bio/Tools/Run/PiseApplication/recoder.pm
Bio/Tools/Run/PiseApplication/redata.pm
Bio/Tools/Run/PiseApplication/remap.pm
Bio/Tools/Run/PiseApplication/repeats.pm
Bio/Tools/Run/PiseApplication/restover.pm
Bio/Tools/Run/PiseApplication/restrict.pm
Bio/Tools/Run/PiseApplication/revseq.pm
Bio/Tools/Run/PiseApplication/rnadistance.pm
Bio/Tools/Run/PiseApplication/rnaeval.pm
Bio/Tools/Run/PiseApplication/rnafold.pm
Bio/Tools/Run/PiseApplication/rnaga.pm
Bio/Tools/Run/PiseApplication/rnaheat.pm
Bio/Tools/Run/PiseApplication/rnainverse.pm
Bio/Tools/Run/PiseApplication/rnapdist.pm
Bio/Tools/Run/PiseApplication/rnasubopt.pm
Bio/Tools/Run/PiseApplication/sam2hmmer.pm
Bio/Tools/Run/PiseApplication/sampleseqs.pm
Bio/Tools/Run/PiseApplication/saps.pm
Bio/Tools/Run/PiseApplication/satellites.pm
Bio/Tools/Run/PiseApplication/scan_for_matches.pm
Bio/Tools/Run/PiseApplication/scope.pm
Bio/Tools/Run/PiseApplication/scopparse.pm
Bio/Tools/Run/PiseApplication/seqboot.pm
Bio/Tools/Run/PiseApplication/seqgen.pm
Bio/Tools/Run/PiseApplication/seqmatchall.pm
Bio/Tools/Run/PiseApplication/seqsblast.pm
Bio/Tools/Run/PiseApplication/seqstat.pm
Bio/Tools/Run/PiseApplication/showalign.pm
Bio/Tools/Run/PiseApplication/showfeat.pm
Bio/Tools/Run/PiseApplication/showorf.pm
Bio/Tools/Run/PiseApplication/showseq.pm
Bio/Tools/Run/PiseApplication/shuffleseq.pm
Bio/Tools/Run/PiseApplication/sigcleave.pm
Bio/Tools/Run/PiseApplication/siggen.pm
Bio/Tools/Run/PiseApplication/sigscan.pm
Bio/Tools/Run/PiseApplication/silent.pm
Bio/Tools/Run/PiseApplication/sirna.pm
Bio/Tools/Run/PiseApplication/splitter.pm
Bio/Tools/Run/PiseApplication/sreformat.pm
Bio/Tools/Run/PiseApplication/stretcher.pm
Bio/Tools/Run/PiseApplication/stride.pm
Bio/Tools/Run/PiseApplication/stssearch.pm
Bio/Tools/Run/PiseApplication/supermatcher.pm
Bio/Tools/Run/PiseApplication/syco.pm
Bio/Tools/Run/PiseApplication/tacg.pm
Bio/Tools/Run/PiseApplication/tfscan.pm
Bio/Tools/Run/PiseApplication/tipdate.pm
Bio/Tools/Run/PiseApplication/tmap.pm
Bio/Tools/Run/PiseApplication/toppred.pm
Bio/Tools/Run/PiseApplication/tranalign.pm
Bio/Tools/Run/PiseApplication/transeq.pm
Bio/Tools/Run/PiseApplication/treealign.pm
Bio/Tools/Run/PiseApplication/trimest.pm
Bio/Tools/Run/PiseApplication/trimseq.pm
Bio/Tools/Run/PiseApplication/trnascan.pm
Bio/Tools/Run/PiseApplication/twofeat.pm
Bio/Tools/Run/PiseApplication/unroot.pm
Bio/Tools/Run/PiseApplication/vectorstrip.pm
Bio/Tools/Run/PiseApplication/water.pm
Bio/Tools/Run/PiseApplication/weighbor.pm
Bio/Tools/Run/PiseApplication/whichdb.pm
Bio/Tools/Run/PiseApplication/wise2.pm
Bio/Tools/Run/PiseApplication/wobble.pm
Bio/Tools/Run/PiseApplication/wordcount.pm
Bio/Tools/Run/PiseApplication/wordmatch.pm
Bio/Tools/Run/PiseApplication/wublast2.pm
Bio/Tools/Run/PiseApplication/xblast.pm
Bio/Tools/Run/PiseApplication/xpound.pm
Bio/Tools/Run/PiseJob.pm
Bio/Tools/Run/PiseJobParser.pm
Bio/Tools/Run/PiseWorkflow.pm
Bio/Tools/Run/Primate.pm
Bio/Tools/Run/Primer3.pm
Bio/Tools/Run/Prints.pm
Bio/Tools/Run/Profile.pm
Bio/Tools/Run/Promoterwise.pm
Bio/Tools/Run/Pseudowise.pm
Bio/Tools/Run/RepeatMasker.pm
Bio/Tools/Run/Seg.pm
Bio/Tools/Run/Signalp.pm
Bio/Tools/Run/Tmhmm.pm
Bio/Tools/Run/TribeMCL.pm
Bio/Tools/Run/Vista.pm
Changes
examples/pise/blast-kun.pl
examples/pise/blast2.pl
examples/pise/clustalw.pl
examples/pise/dnadist.data
examples/pise/dnadist.pl
examples/pise/genscan.pl
examples/pise/needle.pl
examples/pise/phylo-kun.pl
examples/pise/toppred.pl
INSTALL.PROGRAMS
MANIFEST			This list of files
README
scripts/panalysis.PLS
scripts/papplmaker.PLS
scripts/run_neighbor.PLS
scripts/run_protdist.PLS
t/Analysis_soap.t
t/AnalysisFactory_soap.t
t/Blat.t
t/Clustalw.t
t/Coil.t
t/Consense.t
t/data/amino.fa
t/data/blat_dna.fa
t/data/cel-cbr-fam.aln
t/data/codeml.mlc
t/data/coil_protein_input
t/data/consense.treefile
t/data/cysprot.fa
t/data/cysprot.msf
t/data/cysprot1a.fa
t/data/cysprot1a.msf
t/data/cysprot1b.fa
t/data/cysprot1b.msf
t/data/dba1a.fa
t/data/dba1b.fa
t/data/dba2.fa
t/data/dna1.fa
t/data/dna2.fa
t/data/ecolitst.fa
t/data/eponine.fa
t/data/fasta.fa
t/data/fastalib.fa
t/data/fastaprot.fa
t/data/fontfile
t/data/FootPrinter.seq.fa
t/data/Genscan.FastA
t/data/gf-s85.phylip
t/data/hmmpfam_protein_input
t/data/lagan_dna.fa
t/data/new_dna.fa
t/data/new_pep.fa
t/data/NM_002254.gb
t/data/pfam_sample_R11
t/data/primate_query.fa
t/data/primate_target.fa
t/data/Primer3.fa
t/data/prints.dat
t/data/Prints_prot.FastA
t/data/profile_prot.FastA
t/data/prosite.dat
t/data/protpars.phy
t/data/ps1.fa
t/data/repeatmasker.fa
t/data/repeatmasker.fa.out
t/data/signalp_input_protein
t/data/sim4_cdna.fa
t/data/sim4_database.fa
t/data/sim4_genomic.fa
t/data/test.txt
t/data/test_prot.FastA
t/data/tree_of_life
t/data/treefile.example
t/data/TribeMCL.bls
t/data/TribeMCL.desc
t/data/vista.cls
t/data/vista.gff
t/DBA.t
t/DrawGram.t
t/DrawTree.t
t/EMBOSS.t
t/Eponine.t
t/FootPrinter.t
t/Genewise.t
t/Genscan.t
t/Hmmer.t
t/Hmmpfam.t
t/Lagan.t
t/Mdust.t
t/Molphy.t
t/Neighbor.t
t/PAML.t
t/Pise.t
t/Primate.t
t/Primer3.t
t/Prints.t
t/Profile.t
t/Promoterwise.t
t/ProtDist.t
t/ProtPars.t
t/Pseudowise.t
t/RepeatMasker.t
t/Seg.t
t/SeqBoot.t
t/Signalp.t
t/Sim4.t
t/StandAloneFasta.t
t/TCoffee.t
t/Tmhmm.t
t/TribeMCL.t
t/Vista.t
