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1.28
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desc
@@


1.28
log
@- Update to 6.2.0

Submitted by:	Wen Heping(myself)
Approved by:	maintainer(via Email)
@
text
@bin/aaindexextract
bin/abiview
bin/acdc
bin/acdpretty
bin/acdtable
bin/acdtrace
bin/acdvalid
bin/aligncopy
bin/aligncopypair
bin/antigenic
bin/backtranambig
bin/backtranseq
bin/banana
bin/biosed
bin/btwisted
bin/cai
bin/chaos
bin/charge
bin/checktrans
bin/chips
bin/cirdna
bin/codcmp
bin/codcopy
bin/coderet
bin/compseq
bin/cons
bin/consambig
bin/cpgplot
bin/cpgreport
bin/cusp
bin/cutgextract
bin/cutseq
bin/dan
bin/dbiblast
bin/dbifasta
bin/dbiflat
bin/dbigcg
bin/dbxfasta
bin/dbxflat
bin/dbxgcg
bin/degapseq
bin/density
bin/descseq
bin/diffseq
bin/digest
bin/distmat
bin/dotmatcher
bin/dotpath
bin/dottup
bin/dreg
bin/edialign
bin/einverted
bin/embossdata
bin/embossversion
bin/emma
bin/emowse
bin/entret
bin/epestfind
bin/eprimer3
bin/equicktandem
bin/est2genome
bin/etandem
bin/extractalign
bin/extractfeat
bin/extractseq
bin/featcopy
bin/featreport
bin/findkm
bin/freak
bin/fuzznuc
bin/fuzzpro
bin/fuzztran
bin/garnier
bin/geecee
bin/getorf
bin/helixturnhelix
bin/hmoment
bin/iep
bin/infoalign
bin/infobase
bin/inforesidue
bin/infoseq
bin/isochore
bin/jaspextract
bin/jaspscan
bin/jembossctl
bin/lindna
bin/listor
bin/makenucseq
bin/makeprotseq
bin/marscan
bin/maskambignuc
bin/maskambigprot
bin/maskfeat
bin/maskseq
bin/matcher
bin/megamerger
bin/merger
bin/msbar
bin/mwcontam
bin/mwfilter
bin/needle
bin/needleall
bin/newcpgreport
bin/newcpgseek
bin/newseq
bin/nohtml
bin/noreturn
bin/nospace
bin/notab
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bin/nthseq
bin/nthseqset
bin/octanol
bin/oddcomp
bin/palindrome
bin/pasteseq
bin/patmatdb
bin/patmatmotifs
bin/pepcoil
bin/pepinfo
bin/pepnet
bin/pepstats
bin/pepwheel
bin/pepwindow
bin/pepwindowall
bin/plotcon
bin/plotorf
bin/polydot
bin/preg
bin/prettyplot
bin/prettyseq
bin/primersearch
bin/printsextract
bin/profit
bin/prophecy
bin/prophet
bin/prosextract
bin/pscan
bin/psiphi
bin/rebaseextract
bin/recoder
bin/redata
bin/remap
bin/restover
bin/restrict
bin/revseq
bin/runJemboss.csh
bin/seealso
bin/seqmatchall
bin/seqret
bin/seqretsetall
bin/seqretsplit
bin/showalign
bin/showdb
bin/showfeat
bin/showorf
bin/showpep
bin/showseq
bin/shuffleseq
bin/sigcleave
bin/silent
bin/sirna
bin/sixpack
bin/sizeseq
bin/skipredundant
bin/skipseq
bin/splitsource
bin/splitter
bin/stretcher
bin/stssearch
bin/supermatcher
bin/syco
bin/tcode
bin/textsearch
bin/tfextract
bin/tfm
bin/tfscan
bin/tmap
bin/tranalign
bin/transeq
bin/trimest
bin/trimseq
bin/trimspace
bin/twofeat
bin/union
bin/vectorstrip
bin/water
bin/whichdb
bin/wobble
bin/wordcount
bin/wordfinder
bin/wordmatch
bin/wossname
bin/yank
include/ajacd.h
include/ajalign.h
include/ajarch.h
include/ajarr.h
include/ajassert.h
include/ajax.h
include/ajbase.h
include/ajcall.h
include/ajcod.h
include/ajdan.h
include/ajdefine.h
include/ajdmx.h
include/ajdom.h
include/ajdomain.h
include/ajexcept.h
include/ajfeat.h
include/ajfeatdata.h
include/ajfile.h
include/ajfiledata.h
include/ajfileio.h
include/ajfmt.h
include/ajgraph.h
include/ajgraphstruct.h
include/ajhist.h
include/ajindex.h
include/ajjava.h
include/ajlist.h
include/ajmath.h
include/ajmatrices.h
include/ajmem.h
include/ajmess.h
include/ajnam.h
include/ajnexus.h
include/ajpat.h
include/ajpdb.h
include/ajpdbio.h
include/ajphylo.h
include/ajrange.h
include/ajreg.h
include/ajreport.h
include/ajseq.h
include/ajseqabi.h
include/ajseqdata.h
include/ajseqdb.h
include/ajseqread.h
include/ajseqtype.h
include/ajseqwrite.h
include/ajsort.h
include/ajsql.h
include/ajstr.h
include/ajsys.h
include/ajtable.h
include/ajtime.h
include/ajtranslate.h
include/ajtree.h
include/ajutil.h
include/ajvector.h
include/crc32.h
include/deflate.h
include/embaln.h
include/embcom.h
include/embcons.h
include/embdata.h
include/embdbi.h
include/embdmx.h
include/embdomain.h
include/embest.h
include/embexit.h
include/embgroup.h
include/embiep.h
include/embindex.h
include/embinit.h
include/embmat.h
include/embmisc.h
include/embmol.h
include/embnmer.h
include/emboss.h
include/embpat.h
include/embpatlist.h
include/embpdb.h
include/embprop.h
include/embread.h
include/embshow.h
include/embsig.h
include/embword.h
include/ensanalysis.h
include/ensassemblyexception.h
include/ensassembly.h
include/ensassemblymapper.h
include/ensattribute.h
include/ensbaseadaptor.h
include/enscache.h
include/enscoordsystem.h
include/ensdatabaseadaptor.h
include/ensdatabaseconnection.h
include/ensdatabaseentry.h
include/ensdata.h
include/ensdensity.h
include/ensditag.h
include/ensembl.h
include/ensexon.h
include/ensexternaldatabase.h
include/ensfeature.h
include/ensgene.h
include/ensgvdata.h
include/ensgvindividual.h
include/ensgvpopulation.h
include/ensgvsample.h
include/ensintron.h
include/enskaryotype.h
include/ensmapper.h
include/ensmarker.h
include/ensmetacoordinate.h
include/ensmetainformation.h
include/ensmiscellaneous.h
include/ensprediction.h
include/ensprojectionsegment.h
include/ensqcalignment.h
include/ensqcdatabase.h
include/ensqc.h
include/ensqcsequence.h
include/ensregistry.h
include/ensrepeat.h
include/ensseqregion.h
include/enssequence.h
include/enssequenceedit.h
include/ensslice.h
include/ensstorable.h
include/enstable.h
include/enstranslation.h
include/enstranscript.h
include/ensutility.h
include/ensvariation.h
include/eplplot/disptab.h
include/eplplot/drivers.h
include/eplplot/metadefs.h
include/eplplot/pdf.h
include/eplplot/plConfig.h
include/eplplot/plDevs.h
include/eplplot/plcore.h
include/eplplot/pldebug.h
include/eplplot/pldll.h
include/eplplot/plevent.h
include/eplplot/plfci-type1.h
include/eplplot/plhershey-unicode.h
include/eplplot/plplot.h
include/eplplot/plplotP.h
include/eplplot/plstrm.h
include/eplplot/plunicode-type1.h
include/eplplot/plxwd.h
include/eplplot/ps.h
include/expat.h
include/expat_external.h
include/expatemboss.h
include/inffast.h
include/inffixed.h
include/inflate.h
include/inftrees.h
include/pcre.h
include/pcre_config.h
include/pcreemboss.h
include/pcre_internal.h
include/pcre_printint.src
include/pcreposix.h
include/trees.h
include/ucp.h
include/zconf.h
include/zlibemboss.h
include/zlib.h
include/zutil.h
lib/libacd.so.6
lib/libacd.so
lib/libacd.la
lib/libacd.a
lib/libajax.a
lib/libajax.la
lib/libajax.so
lib/libajax.so.6
lib/libajaxdb.a
lib/libajaxdb.la
lib/libajaxdb.so
lib/libajaxdb.so.6
lib/libajaxg.a
lib/libajaxg.la
lib/libajaxg.so
lib/libajaxg.so.6
lib/libeexpat.a
lib/libeexpat.la
lib/libeexpat.so
lib/libeexpat.so.2
lib/libensembl.a
lib/libensembl.la
lib/libensembl.so
lib/libensembl.so.6
lib/libepcre.a
lib/libepcre.la
lib/libepcre.so
lib/libepcre.so.7
lib/libeplplot.a
lib/libeplplot.la
lib/libeplplot.so
lib/libeplplot.so.5
lib/libezlib.a
lib/libezlib.la
lib/libezlib.so
lib/libezlib.so.2
lib/libnucleus.a
lib/libnucleus.la
lib/libnucleus.so
lib/libnucleus.so.6
%%DATADIR%%/acd/aaindexextract.acd
%%DATADIR%%/acd/abiview.acd
%%DATADIR%%/acd/acdc.acd
%%DATADIR%%/acd/acdlog.acd
%%DATADIR%%/acd/acdpretty.acd
%%DATADIR%%/acd/acdrelations.acd
%%DATADIR%%/acd/acdtable.acd
%%DATADIR%%/acd/acdtrace.acd
%%DATADIR%%/acd/acdvalid.acd
%%DATADIR%%/acd/ajbad.acd
%%DATADIR%%/acd/ajfeatest.acd
%%DATADIR%%/acd/ajtest.acd
%%DATADIR%%/acd/aligncopy.acd
%%DATADIR%%/acd/aligncopypair.acd
%%DATADIR%%/acd/antigenic.acd
%%DATADIR%%/acd/backtranambig.acd
%%DATADIR%%/acd/backtranseq.acd
%%DATADIR%%/acd/banana.acd
%%DATADIR%%/acd/biosed.acd
%%DATADIR%%/acd/btwisted.acd
%%DATADIR%%/acd/cai.acd
%%DATADIR%%/acd/chaos.acd
%%DATADIR%%/acd/charge.acd
%%DATADIR%%/acd/checktrans.acd
%%DATADIR%%/acd/chips.acd
%%DATADIR%%/acd/cirdna.acd
%%DATADIR%%/acd/codcmp.acd
%%DATADIR%%/acd/codcopy.acd
%%DATADIR%%/acd/coderet.acd
%%DATADIR%%/acd/codes.english
%%DATADIR%%/acd/complex.acd
%%DATADIR%%/acd/compseq.acd
%%DATADIR%%/acd/cons.acd
%%DATADIR%%/acd/consambig.acd
%%DATADIR%%/acd/corbatest.acd
%%DATADIR%%/acd/cpgplot.acd
%%DATADIR%%/acd/cpgreport.acd
%%DATADIR%%/acd/cusp.acd
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%%DATADIR%%/acd/cutseq.acd
%%DATADIR%%/acd/dan.acd
%%DATADIR%%/acd/dbiblast.acd
%%DATADIR%%/acd/dbifasta.acd
%%DATADIR%%/acd/dbiflat.acd
%%DATADIR%%/acd/dbigcg.acd
%%DATADIR%%/acd/dbxfasta.acd
%%DATADIR%%/acd/dbxflat.acd
%%DATADIR%%/acd/dbxgcg.acd
%%DATADIR%%/acd/dbxreport.acd
%%DATADIR%%/acd/dbxstat.acd
%%DATADIR%%/acd/degapseq.acd
%%DATADIR%%/acd/density.acd
%%DATADIR%%/acd/descseq.acd
%%DATADIR%%/acd/diffseq.acd
%%DATADIR%%/acd/digest.acd
%%DATADIR%%/acd/distmat.acd
%%DATADIR%%/acd/dotmatcher.acd
%%DATADIR%%/acd/dotpath.acd
%%DATADIR%%/acd/dottup.acd
%%DATADIR%%/acd/dreg.acd
%%DATADIR%%/acd/edamclean.acd
%%DATADIR%%/acd/edialign.acd
%%DATADIR%%/acd/einverted.acd
%%DATADIR%%/acd/embossdata.acd
%%DATADIR%%/acd/embossversion.acd
%%DATADIR%%/acd/emma.acd
%%DATADIR%%/acd/emowse.acd
%%DATADIR%%/acd/ensembltest.acd
%%DATADIR%%/acd/entrails.acd
%%DATADIR%%/acd/entret.acd
%%DATADIR%%/acd/epestfind.acd
%%DATADIR%%/acd/eprimer3.acd
%%DATADIR%%/acd/equicktandem.acd
%%DATADIR%%/acd/est2genome.acd
%%DATADIR%%/acd/etandem.acd
%%DATADIR%%/acd/extractalign.acd
%%DATADIR%%/acd/extractfeat.acd
%%DATADIR%%/acd/extractseq.acd
%%DATADIR%%/acd/featcopy.acd
%%DATADIR%%/acd/featreport.acd
%%DATADIR%%/acd/findkm.acd
%%DATADIR%%/acd/freak.acd
%%DATADIR%%/acd/fuzznuc.acd
%%DATADIR%%/acd/fuzzpro.acd
%%DATADIR%%/acd/fuzztran.acd
%%DATADIR%%/acd/garnier.acd
%%DATADIR%%/acd/geecee.acd
%%DATADIR%%/acd/getorf.acd
%%DATADIR%%/acd/groups.standard
%%DATADIR%%/acd/helixturnhelix.acd
%%DATADIR%%/acd/histogramtest.acd
%%DATADIR%%/acd/hmoment.acd
%%DATADIR%%/acd/iep.acd
%%DATADIR%%/acd/infoalign.acd
%%DATADIR%%/acd/infobase.acd
%%DATADIR%%/acd/inforesidue.acd
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%%DATADIR%%/acd/intconv.acd
%%DATADIR%%/acd/isochore.acd
%%DATADIR%%/acd/jaspextract.acd
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%%DATADIR%%/acd/keywords.standard
%%DATADIR%%/acd/knowntypes.standard
%%DATADIR%%/acd/lindna.acd
%%DATADIR%%/acd/listor.acd
%%DATADIR%%/acd/makenucseq.acd
%%DATADIR%%/acd/makeprotseq.acd
%%DATADIR%%/acd/marscan.acd
%%DATADIR%%/acd/maskambignuc.acd
%%DATADIR%%/acd/maskambigprot.acd
%%DATADIR%%/acd/maskfeat.acd
%%DATADIR%%/acd/maskseq.acd
%%DATADIR%%/acd/matcher.acd
%%DATADIR%%/acd/megamerger.acd
%%DATADIR%%/acd/merger.acd
%%DATADIR%%/acd/msbar.acd
%%DATADIR%%/acd/mwcontam.acd
%%DATADIR%%/acd/mwfilter.acd
%%DATADIR%%/acd/needle.acd
%%DATADIR%%/acd/needleall.acd
%%DATADIR%%/acd/newcoils.acd
%%DATADIR%%/acd/newcpgreport.acd
%%DATADIR%%/acd/newcpgseek.acd
%%DATADIR%%/acd/newseq.acd
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%%DATADIR%%/acd/nthseq.acd
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%%DATADIR%%/acd/octanol.acd
%%DATADIR%%/acd/oddcomp.acd
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%%DATADIR%%/acd/origunion.acd
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%%DATADIR%%/acd/patmatdb.acd
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%%DATADIR%%/acd/patmattest.acd
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%%DATADIR%%/acd/pepinfo.acd
%%DATADIR%%/acd/pepnet.acd
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%%DATADIR%%/acd/pepwheel.acd
%%DATADIR%%/acd/pepwindow.acd
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%%DATADIR%%/acd/plotcon.acd
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%%DATADIR%%/acd/primers.acd
%%DATADIR%%/acd/primersearch.acd
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%%DATADIR%%/test/data/dna.staden
%%DATADIR%%/test/data/dna.strider
%%DATADIR%%/test/data/dna.text
%%DATADIR%%/test/data/feat.emft
%%DATADIR%%/test/data/feat.fasta
%%DATADIR%%/test/data/feat.pir
%%DATADIR%%/test/data/mw1.dat
%%DATADIR%%/test/data/mw2.dat
%%DATADIR%%/test/data/mw3.dat
%%DATADIR%%/test/data/nuc.pat
%%DATADIR%%/test/data/nucseq.pat
%%DATADIR%%/test/data/nucsimple.pat
%%DATADIR%%/test/data/opsd.msf
%%DATADIR%%/test/data/paamir.gff
%%DATADIR%%/test/data/paamir.gff3
%%DATADIR%%/test/data/paamir.pep
%%DATADIR%%/test/data/pax6_cdna.fasta
%%DATADIR%%/test/data/prints.test
%%DATADIR%%/test/data/prosite.dat
%%DATADIR%%/test/data/prosite.doc
%%DATADIR%%/test/data/prot.acedb
%%DATADIR%%/test/data/prot.codata
%%DATADIR%%/test/data/prot.fasta
%%DATADIR%%/test/data/prot.gcg
%%DATADIR%%/test/data/prot.gcg8
%%DATADIR%%/test/data/prot.ig
%%DATADIR%%/test/data/prot.m-acedb
%%DATADIR%%/test/data/prot.m-codata
%%DATADIR%%/test/data/prot.m-fasta
%%DATADIR%%/test/data/prot.m-nbrf
%%DATADIR%%/test/data/prot.m-ncbi
%%DATADIR%%/test/data/prot.m-swiss
%%DATADIR%%/test/data/prot.nbrf
%%DATADIR%%/test/data/prot.ncbi
%%DATADIR%%/test/data/prot.swiss
%%DATADIR%%/test/data/prot.text
%%DATADIR%%/test/data/site.dat
%%DATADIR%%/test/data/tranalign.pep
%%DATADIR%%/test/data/tranalign.seq
%%DATADIR%%/test/data/untrimmed.seq
%%DATADIR%%/test/data/vtest.seq
%%DATADIR%%/test/data/withrefm
%%DATADIR%%/test/data/z83307.seq
%%DATADIR%%/test/embl/acnum.hit
%%DATADIR%%/test/embl/acnum.trg
%%DATADIR%%/test/embl/des.hit
%%DATADIR%%/test/embl/des.trg
%%DATADIR%%/test/embl/division.lkp
%%DATADIR%%/test/embl/entrynam.idx
%%DATADIR%%/test/embl/est.dat
%%DATADIR%%/test/embl/fun.dat
%%DATADIR%%/test/embl/hum1.dat
%%DATADIR%%/test/embl/inv.dat
%%DATADIR%%/test/embl/keyword.hit
%%DATADIR%%/test/embl/keyword.trg
%%DATADIR%%/test/embl/pln.dat
%%DATADIR%%/test/embl/pro.dat
%%DATADIR%%/test/embl/rod.dat
%%DATADIR%%/test/embl/seqvn.hit
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%%DATADIR%%/test/embl/sts.dat
%%DATADIR%%/test/embl/taxon.hit
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%%DATADIR%%/test/embl/vrl.dat
%%DATADIR%%/test/embl/vrt.dat
%%DATADIR%%/test/genbank/acnum.hit
%%DATADIR%%/test/genbank/acnum.trg
%%DATADIR%%/test/genbank/des.hit
%%DATADIR%%/test/genbank/des.trg
%%DATADIR%%/test/genbank/division.lkp
%%DATADIR%%/test/genbank/entrynam.idx
%%DATADIR%%/test/genbank/gbbct1.seq
%%DATADIR%%/test/genbank/gbest1.seq
%%DATADIR%%/test/genbank/gbinv1.seq
%%DATADIR%%/test/genbank/gbpln1.seq
%%DATADIR%%/test/genbank/gbpln2.seq
%%DATADIR%%/test/genbank/gbpri1.seq
%%DATADIR%%/test/genbank/gbrod1.seq
%%DATADIR%%/test/genbank/gbsts1.seq
%%DATADIR%%/test/genbank/gbvrl1.seq
%%DATADIR%%/test/genbank/gbvrt.seq
%%DATADIR%%/test/genbank/keyword.hit
%%DATADIR%%/test/genbank/keyword.trg
%%DATADIR%%/test/genbank/seqvn.hit
%%DATADIR%%/test/genbank/seqvn.trg
%%DATADIR%%/test/genbank/taxon.hit
%%DATADIR%%/test/genbank/taxon.trg
%%DATADIR%%/test/pir/acnum.hit
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%%DATADIR%%/test/pir/des.hit
%%DATADIR%%/test/pir/des.trg
%%DATADIR%%/test/pir/division.lkp
%%DATADIR%%/test/pir/entrynam.idx
%%DATADIR%%/test/pir/keyword.hit
%%DATADIR%%/test/pir/keyword.trg
%%DATADIR%%/test/pir/pir1.header
%%DATADIR%%/test/pir/pir1.names
%%DATADIR%%/test/pir/pir1.numbers
%%DATADIR%%/test/pir/pir1.offset
%%DATADIR%%/test/pir/pir1.ref
%%DATADIR%%/test/pir/pir1.seq
%%DATADIR%%/test/pir/pir2.header
%%DATADIR%%/test/pir/pir2.names
%%DATADIR%%/test/pir/pir2.numbers
%%DATADIR%%/test/pir/pir2.offset
%%DATADIR%%/test/pir/pir2.ref
%%DATADIR%%/test/pir/pir2.seq
%%DATADIR%%/test/pir/pir3.header
%%DATADIR%%/test/pir/pir3.names
%%DATADIR%%/test/pir/pir3.numbers
%%DATADIR%%/test/pir/pir3.offset
%%DATADIR%%/test/pir/pir3.ref
%%DATADIR%%/test/pir/pir3.seq
%%DATADIR%%/test/pir/pir4.header
%%DATADIR%%/test/pir/pir4.names
%%DATADIR%%/test/pir/pir4.numbers
%%DATADIR%%/test/pir/pir4.offset
%%DATADIR%%/test/pir/pir4.ref
%%DATADIR%%/test/pir/pir4.seq
%%DATADIR%%/test/pir/taxon.hit
%%DATADIR%%/test/pir/taxon.trg
%%DATADIR%%/test/swiss/acnum.hit
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%%DATADIR%%/test/swiss/des.hit
%%DATADIR%%/test/swiss/des.trg
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%%DATADIR%%/test/swiss/entrynam.idx
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%%DATADIR%%/test/swiss/keyword.trg
%%DATADIR%%/test/swiss/seq.dat
%%DATADIR%%/test/swiss/seqvn.hit
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%%DATADIR%%/test/swiss/taxon.hit
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%%DATADIR%%/test/swnew/acnum.hit
%%DATADIR%%/test/swnew/acnum.trg
%%DATADIR%%/test/swnew/des.hit
%%DATADIR%%/test/swnew/des.trg
%%DATADIR%%/test/swnew/division.lkp
%%DATADIR%%/test/swnew/entrynam.idx
%%DATADIR%%/test/swnew/keyword.hit
%%DATADIR%%/test/swnew/keyword.trg
%%DATADIR%%/test/swnew/seqvn.hit
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%%DATADIR%%/test/swnew/taxon.trg
%%DATADIR%%/test/swnew/trembl.dat
%%DATADIR%%/test/testdb/acnum.hit
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%%DATADIR%%/test/testdb/des.trg
%%DATADIR%%/test/testdb/division.lkp
%%DATADIR%%/test/testdb/entrynam.idx
%%DATADIR%%/test/testdb/testdb.fasta
@@dirrm bin
@@dirrm include/eplplot
@@dirrm include
@@dirrm lib
@@dirrm %%DATADIR%%/acd
@@dirrm %%DATADIR%%/data/AAINDEX
@@dirrm %%DATADIR%%/data/CODONS
@@dirrm %%DATADIR%%/data/JASPAR_CNE
@@dirrm %%DATADIR%%/data/JASPAR_CORE
@@dirrm %%DATADIR%%/data/JASPAR_FAM
@@dirrm %%DATADIR%%/data/JASPAR_PHYLOFACTS
@@dirrm %%DATADIR%%/data/JASPAR_POLII
@@dirrm %%DATADIR%%/data/JASPAR_SPLICE
@@dirrm %%DATADIR%%/data/PRINTS
@@dirrm %%DATADIR%%/data/PROSITE
@@dirrm %%DATADIR%%/data/REBASE
@@dirrm %%DATADIR%%/data
@@dirrm %%DOCSDIR%%/manuals
@@dirrm %%DOCSDIR%%/programs/html
@@dirrm %%DOCSDIR%%/programs/text
@@dirrm %%DOCSDIR%%/programs
@@dirrm %%DOCSDIR%%/tutorials
@@dirrm %%DOCSDIR%%
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss
@@dirrm %%DATADIR%%/jemboss/api/org/emboss
@@dirrm %%DATADIR%%/jemboss/api/org
@@dirrm %%DATADIR%%/jemboss/api
@@dirrm %%DATADIR%%/jemboss/images
@@dirrm %%DATADIR%%/jemboss/lib/axis
@@dirrm %%DATADIR%%/jemboss/lib
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss
@@dirrm %%DATADIR%%/jemboss/org/emboss
@@dirrm %%DATADIR%%/jemboss/org
@@dirrm %%DATADIR%%/jemboss/resources
@@dirrm %%DATADIR%%/jemboss/utils
@@dirrm %%DATADIR%%/jemboss
@@dirrm %%DATADIR%%/test/data
@@dirrm %%DATADIR%%/test/embl
@@dirrm %%DATADIR%%/test/genbank
@@dirrm %%DATADIR%%/test/pir
@@dirrm %%DATADIR%%/test/swiss
@@dirrm %%DATADIR%%/test/swnew
@@dirrm %%DATADIR%%/test/testdb
@@dirrm %%DATADIR%%/test
@@dirrm %%DATADIR%%
@@dirrmtry share
@


1.27
log
@- Force commit to correct the entry
- Update to 6.0.1

PR:		132504
Submitted by:	Wen Heping <wenheping@@gmail.com>
Approved by:	maintainer
@
text
@d103 1
d113 1
d152 1
d158 1
d168 1
a218 1
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d244 1
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%%DATADIR%%/acd/giep.acd
d500 2
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%%DOCSDIR%%/programs/text/frestdist.txt
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%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar
a1638 1
%%DATADIR%%/jemboss/lib/grout.jar
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%%DATADIR%%/jemboss/lib/jalview.jar
a1642 1
%%DATADIR%%/jemboss/lib/xerces.jar
d1787 1
d1794 1
@


1.26
log
@- Update to 0.1.24

PR:		132527
Submitted by:	Wen Heping <wenheping@@gmail.com>
Approved by:	maintainer
@
text
@@


1.25
log
@- Update to 5.0.0

PR:		ports/122437
Submitted by:	Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
@
text
@d8 2
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%%PORTDOCS%%@@dirrm %%DOCSDIR%%/html/emboss
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/html
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@


1.24
log
@- Sort pkg-plist before updating to 5.0.0

PR:		ports/122437
Submitted by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
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%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
a569 2
%%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/allversusall.txt
d571 1
a576 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt
a584 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/comparator.txt
a587 2
%%PORTDOCS%%%%DOCSDIR%%/programs/text/contactalign.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt
a589 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/crystalball.txt
a601 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseqrunner.txt
a605 7
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainalign.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainnr.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainrep.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainreso.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainseqs.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainsse.txt
d610 1
a610 26
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ealistat.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/eclique.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/econsense.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtrast.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednacomp.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednadist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednainvar.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednaml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednamlk.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/egendist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmalign.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmbuild.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmcalibrate.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmconvert.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmemit.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmfetch.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmindex.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmpfam.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ehmmsearch.txt
a611 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ekitsch.txt
a613 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/emix.txt
a614 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/emnu.txt
a615 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/eneighbor.txt
a616 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/epenny.txt
a618 2
%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotdist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotpars.txt
a619 3
%%PORTDOCS%%%%DOCSDIR%%/programs/text/erestml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/eseqboot.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/esim4.txt
a623 22
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fclique.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fconsense.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fcontrast.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdiscboot.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnacomp.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnadist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnainvar.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnaml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamlk.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnamove.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapars.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdnapenny.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdollop.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolmove.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdolpenny.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawgram.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawtree.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffactor.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffitch.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
a624 10
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fneighbor.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpars.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpenny.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fproml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpromlk.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotdist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotpars.txt
a625 8
%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestboot.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestdist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestml.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fretree.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqboot.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqbootall.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedist.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedistpair.txt
a632 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt
a636 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
a638 2
%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.txt
d641 2
a646 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/matgen3d.txt
a647 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt
a649 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt
a651 3
%%PORTDOCS%%%%DOCSDIR%%/programs/text/myseq.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
a652 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.txt
a664 3
%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbparse.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.txt
a692 7
%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocon.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorecmapdir.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
a693 2
%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
a694 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
a696 3
%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
a703 4
%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggen.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/siggenlig.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscanlig.txt
a705 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
a708 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
a710 2
%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.txt
a718 1
%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt
d730 1
d750 1
d782 1
d790 1
d800 1
d813 1
d834 1
a834 2
%%DATADIR%%/acd/kmrsplitter.acd
%%DATADIR%%/acd/kmrunion.acd
d838 2
d859 2
d943 1
d1303 2
d1328 2
d1342 1
d1344 3
d1526 1
d1602 1
d1643 4
d1671 2
a1696 16
%%DATADIR%%/test/gb/acnum.hit
%%DATADIR%%/test/gb/acnum.trg
%%DATADIR%%/test/gb/ba.ref
%%DATADIR%%/test/gb/ba.seq
%%DATADIR%%/test/gb/des.hit
%%DATADIR%%/test/gb/des.trg
%%DATADIR%%/test/gb/division.lkp
%%DATADIR%%/test/gb/entrynam.idx
%%DATADIR%%/test/gb/htg.ref
%%DATADIR%%/test/gb/htg.seq
%%DATADIR%%/test/gb/keyword.hit
%%DATADIR%%/test/gb/keyword.trg
%%DATADIR%%/test/gb/seqvn.hit
%%DATADIR%%/test/gb/seqvn.trg
%%DATADIR%%/test/gb/taxon.hit
%%DATADIR%%/test/gb/taxon.trg
a1773 1
%%DATADIR%%/test/swnew/new_seq.dat
d1778 10
a1787 15
%%DATADIR%%/test/swnew/upd_ann.dat
%%DATADIR%%/test/swnew/upd_seq.dat
%%DATADIR%%/test/wormpep/acnum.hit
%%DATADIR%%/test/wormpep/acnum.trg
%%DATADIR%%/test/wormpep/des.hit
%%DATADIR%%/test/wormpep/des.trg
%%DATADIR%%/test/wormpep/division.lkp
%%DATADIR%%/test/wormpep/entrynam.idx
%%DATADIR%%/test/wormpep/wormpep
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/manuals
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/programs/html
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/programs/text
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/programs
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/tutorials
%%PORTDOCS%%@@dirrm %%DOCSDIR%%
d1789 5
a1793 5
@@dirrm %%DATADIR%%/data/AAINDEX
@@dirrm %%DATADIR%%/data/CODONS
@@dirrm %%DATADIR%%/data/REBASE
@@dirrm %%DATADIR%%/data/PRINTS
@@dirrm %%DATADIR%%/data/PROSITE
a1797 1
@@dirrm %%DATADIR%%/test/gb
d1801 1
a1801 1
@@dirrm %%DATADIR%%/test/wormpep
d1803 8
a1849 1
@@dirrmtry share/doc
@


1.23
log
@For EMBOSS:

	This patch brings EMBOSS up to date with the current version.

	i.   The patches included in files/ are bugfixes for files in
	     EMBOSS-3.0.0 that appeared after the release. They are
   	     documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README

	     This is just 'for the record' so that we remember to remove these
	     patches in the next update.

	ii.  EMBOSS is now installed by default in LOCALBASE/emboss
	     This is to avoid CONFLICTS with other ports that install files
	     with the same names. Installing EMBOSS to another PREFIX is also
	     possible.

	iii. now EMBASSY and EMBOSS both store their distfiles in the same
	     DIST_SUBDIR

	iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
	     (manual) way

	For EMBASSY:

	This update brings embassy in sync with the update of EMBOSS to 3.0.0.

	Things that changed from previous version of the port:

	i.  embassy now installs by default in $LOCALBASE/emboss (the
	    new default PREFIX for emboss as well).

	ii. changed DIST_SUBDIR so that all the distfiles are put together with
	    emboss. This makes sense(TM)

	iii. incorporated new EMBASSY apps (this accounts for the changes in
	     OPTIONS and pkg-plist)

	iv.  removed obsoleted patches

	Finally, I included a sample text that could go in UPDATING.

PR:		93053
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
@
text
@d28 1
a29 1
bin/cutseq
d126 1
a141 1
bin/syco
d146 1
a166 16
bin/runJemboss.csh
include/drivers.h
include/pdf.h
include/plcore.h
include/plevent.h
include/plplotP.h
include/plxwd.h
include/metadefs.h
include/plConfig.h
include/pldebug.h
include/plplot.h
include/plstrm.h
include/plDevs.h
include/ajax.h
include/ajarch.h
include/ajdefine.h
d169 1
d172 1
d177 1
d186 1
a187 1
include/ajgraphstruct.h
d220 1
a220 8
include/pcre.h
include/pcre_chartables.c
include/pcre_config.h
include/pcre_get.c
include/pcre_printint.c
include/pcre_internal.h
include/pcreposix.h
include/emboss.h
d238 1
d240 1
a241 1
include/embpdb.h
d243 1
a244 1
include/embshow.h
d246 21
a266 4
lib/libplplot.so.5
lib/libplplot.so
lib/libplplot.la
lib/libplplot.a
d268 3
a270 3
lib/libajax.so
lib/libajax.la
lib/libajax.a
d272 3
a274 3
lib/libajaxg.so
lib/libajaxg.la
lib/libajaxg.a
d276 5
a280 5
lib/libnucleus.so
lib/libnucleus.la
lib/libnucleus.a
%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
d286 2
d291 1
a291 2
%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
a293 1
%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
d295 2
a296 160
%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
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@


1.22
log
@Conversion to a single libtool environment.

Approved by:	portmgr (kris)
@
text
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@


1.21
log
@- Update to 2.10.0

PR:		ports/81579
Submitted by:	"Choe, Cheng-Dae" <whitekid@@gmail.com>
Approved by:	Fernan Aguero <fernan@@iib.unsam.edu.ar> (maintainer)
@
text
@d262 1
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@


1.20
log
@- Update to 2.9.0
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
@
text
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bin/noreturn
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a162 1
bin/runJemboss.csh
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include/drivers.h
include/pdf.h
include/plcore.h
include/plevent.h
include/plplotP.h
include/plxwd.h
include/metadefs.h
include/plConfig.h
include/pldebug.h
include/plplot.h
include/plstrm.h
include/plDevs.h
include/ajax.h
include/ajarch.h
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%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
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%%DATADIR%%/jemboss/runJemboss.sh
%%DATADIR%%/jemboss/README
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/manuals
a1927 1
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/programs/text
d1929 1
a1929 1
%%PORTDOCS%%@@dirrm %%DOCSDIR%%/tutorials
d1931 4
a1934 9
@@dirrm %%DATADIR%%/acd
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d1937 2
a1938 4
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d1940 28
a1968 3
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
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a1969 4
@@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd
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a1973 20
@@dirrm %%DATADIR%%/jemboss/images
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@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
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@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser
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@@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap
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@@dirrm %%DATADIR%%/jemboss/org
@@dirrm %%DATADIR%%/jemboss/resources
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d1975 7
@


1.19
log
@Add missing files
@
text
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a1 88
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@


1.18
log
@- Update to version 2.4.1
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)

PR:		40198 ; many private requests
Submitted by:	Tilman Linneweh <tilman@@arved.de> (2.4.1 update)
@
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@


1.17
log
@- Update to version 2.2.0
- Update included EMBASSY package EMNU
- Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from
  being generated properly
- Consider this an interim update merely to track the latest version - more
  work is required to activate the newly included "Jemboss" Java GUI
  interface
@
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share/doc/EMBOSS/programs/text/primer3.txt
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@@dirrm share/EMBOSS/jemboss/embreo/cgi-bin
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@@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo
@@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp
@@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc
@@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac
@@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk
@@dirrm share/EMBOSS/jemboss/embreo/api-docs
@@dirrm share/EMBOSS/jemboss/embreo/Modules
@@dirrm share/EMBOSS/jemboss/embreo
@


1.16
log
@- Update port to version 2.0.1
- Add two new EMBASSY applications, MEME and HMMER.
@
text
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@


1.15
log
@Update to 1.13.3; remove bogus file.

PR:		28119
Reviewed by:	nbm
@
text
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@


1.14
log
@Update to version 1.13.1

PR: 27768
Submitted by: MAINTAINER
@
text
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a1193 1
share/doc/EMBOSS/programs/text/stamps.txt
@


1.13
log
@Update the EMBOSS suite (biology/emboss) to version 1.12.0

PR:		27179
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
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@


1.12
log
@Update the EMBOSS suite to v1.11.0

PR:		25728
Submitted by:	johann@@egenetics.com
@
text
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share/doc/EMBOSS/programs/html/compseq.html
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share/doc/EMBOSS/programs/html/est2genome.html
share/doc/EMBOSS/programs/html/etandem.html
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share/doc/EMBOSS/programs/html/geecee.html
share/doc/EMBOSS/programs/html/gendist.html
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share/doc/EMBOSS/programs/html/getorf.html
share/doc/EMBOSS/programs/html/groups.html
share/doc/EMBOSS/programs/html/helixturnhelix.html
share/doc/EMBOSS/programs/html/hydropathy_group.html
share/doc/EMBOSS/programs/html/iep.html
share/doc/EMBOSS/programs/html/index.html
share/doc/EMBOSS/programs/html/infoseq.html
share/doc/EMBOSS/programs/html/isochore.html
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share/doc/EMBOSS/programs/html/kitsch.html
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@


1.11
log
@Update to version 1.10.1

PR: 25449
Submitted by: maintainer
@
text
@d66 1
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@


1.10
log
@Update to version 1.10.0

PR: 25228
Submitted by: MAINTAINER
@
text
@a70 1
bin/complex
d108 1
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share/doc/EMBOSS/programs/html/complex.html
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@


1.9
log
@- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1
- Update the EMBASSY package EMNU from 1.0.2 to 1.0.3
- Merged the four pkg-plist* files into one

PR: 24717
Submitted by: MAINTAINER
@
text
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1.8
log
@Upgrade to version 1.9.0

PR: 24597
Submitted by: MAINTAINER
@
text
@d1 58
@


1.7
log
@- Update port biology/emboss from 1.7.0 to 1.8.0

PR:		23130
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
@
text
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@


1.6
log
@Update to version 1.7.0

PR:		22474
Submitted by:	Johann Visagie <johann@@egenetics.com> MAINTAINER
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text
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@


1.5
log
@- Update to 1.6.0
- Reorder packing list

PR: 21857
Submitted by: MAINTAINER
@
text
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@


1.4
log
@Upgrade to 1.5.0

PR:		21108
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
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share/EMBOSS/data/Edna.melt
share/EMBOSS/data/Eenergy.dat
share/EMBOSS/data/Efeatures.embl
share/EMBOSS/data/Efeatures.gff
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share/EMBOSS/data/Ehth87.dat
share/EMBOSS/data/Enakai.dat
share/EMBOSS/data/Epepcoil.dat
share/EMBOSS/data/Epprofile
share/EMBOSS/data/Erna.melt
share/EMBOSS/data/Esig.euk
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share/EMBOSS/data/embossre.equ
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share/EMBOSS/test/embl/inv.dat
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share/EMBOSS/test/embl/rod.dat
share/EMBOSS/test/embl/vrl.dat
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@


1.3
log
@Update to emboss 1.4.0.

PR:		ports/20898
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
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@


1.2
log
@Update to emboss 1.1.0, fixing some style bugs too.

PR:		ports/20519
Submitted by:	Johann Visagie <johann@@egenetics.com> (maintainer)
@
text
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@


1.1
log
@Add emboss, the European Molecular Biology Open Software Suite

PR:		ports/20317
Submitted by:	Johann Visagie <johann@@egenetics.com>
@
text
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@

