From 13911bd3b97f7e73d93787bf6f08acb4303edd1c Mon Sep 17 00:00:00 2001 From: jasper Date: Wed, 24 Sep 2008 17:14:26 +0000 Subject: [PATCH] - update emboss to the latest stable version, 6.0.1 --- biology/emboss/Makefile | 12 +- biology/emboss/distinfo | 10 +- biology/emboss/pkg/PLIST | 955 +++++++++++++++++++++------------------ 3 files changed, 532 insertions(+), 445 deletions(-) diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 417a0dc356d..d2a5f47f42f 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -1,13 +1,12 @@ -# $OpenBSD: Makefile,v 1.2 2007/11/06 06:30:32 bernd Exp $ +# $OpenBSD: Makefile,v 1.3 2008/09/24 17:14:26 jasper Exp $ COMMENT= European Molecular Biology Open Software Suite -DISTNAME= EMBOSS-5.0.0 -PKGNAME= ${DISTNAME:L}p0 +DISTNAME= EMBOSS-6.0.1 SHARED_LIBS += eplplot 0.0 # .5.7 -SHARED_LIBS += ajax 0.0 # .5.0 -SHARED_LIBS += ajaxg 0.0 # .5.0 -SHARED_LIBS += nucleus 0.0 # .5.0 +SHARED_LIBS += ajax 1.0 # .6.0 +SHARED_LIBS += ajaxg 1.0 # .6.0 +SHARED_LIBS += nucleus 1.0 # .6.0 CATEGORIES= biology @@ -26,6 +25,7 @@ WANTLIB= X11 Xau Xdmcp c m USE_X11= Yes USE_LIBTOOL= Yes CONFIGURE_STYLE=gnu +CONFIGURE_ARGS+= --without-java CONFIGURE_ENV= CPPFLAGS="-I${LOCALBASE}/include" \ LDFLAGS="-L${LOCALBASE}/lib" diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index fa98d065c48..c9b98fe0f0c 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1,5 +1,5 @@ -MD5 (EMBOSS-5.0.0.tar.gz) = vkyJUiCtNK/WXUULp9jjSw== -RMD160 (EMBOSS-5.0.0.tar.gz) = G/UQwJGdmR5LpnGCE3RI3uSbq00= -SHA1 (EMBOSS-5.0.0.tar.gz) = GtTtxICKgiX+jVdOin0Ghr6ZysY= -SHA256 (EMBOSS-5.0.0.tar.gz) = ZObwm4KnGf8m3n8h/ffSvWBdLGZDhMHHtI+dJF1fQK4= -SIZE (EMBOSS-5.0.0.tar.gz) = 20666560 +MD5 (EMBOSS-6.0.1.tar.gz) = IYKxSNrOa+pAPe7Y+srkDQ== +RMD160 (EMBOSS-6.0.1.tar.gz) = yXZzZwoRC1GmwdGgMFRRxEzXtQQ= +SHA1 (EMBOSS-6.0.1.tar.gz) = 6m+m4eQiK8V+dIpNZ01y2bA0dd0= +SHA256 (EMBOSS-6.0.1.tar.gz) = PjUpAqqdq4i/SGRX/yN5Txk5jfxrVQxL8XXfytNMIz0= +SIZE (EMBOSS-6.0.1.tar.gz) = 20204153 diff --git a/biology/emboss/pkg/PLIST b/biology/emboss/pkg/PLIST index 774ed847923..5e5961d750c 100644 --- a/biology/emboss/pkg/PLIST +++ b/biology/emboss/pkg/PLIST @@ -1,178 +1,196 @@ -@comment $OpenBSD: PLIST,v 1.2 2007/11/06 06:30:32 bernd Exp $ +@comment $OpenBSD: PLIST,v 1.3 2008/09/24 17:14:26 jasper Exp $ @conflict pscan-* %%SHARED%% -bin/aaindexextract -bin/abiview -bin/acdc -bin/acdpretty -bin/acdtable -bin/acdtrace -bin/acdvalid -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/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/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/findkm -bin/freak -bin/fuzznuc -bin/fuzzpro -bin/fuzztran -bin/garnier -bin/geecee -bin/getorf -bin/helixturnhelix -bin/hmoment -bin/iep -bin/infoalign -bin/infoseq -bin/isochore -bin/jembossctl -bin/lindna -bin/listor -bin/makenucseq -bin/makeprotseq -bin/marscan -bin/maskfeat -bin/maskseq -bin/matcher -bin/megamerger -bin/merger -bin/msbar -bin/mwcontam -bin/mwfilter -bin/needle -bin/newcpgreport -bin/newcpgseek -bin/newseq -bin/noreturn -bin/notseq -bin/nthseq -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 bin/aaindexextract +@bin bin/abiview +@bin bin/acdc +@bin bin/acdpretty +@bin bin/acdtable +@bin bin/acdtrace +@bin bin/acdvalid +@bin bin/aligncopy +@bin bin/aligncopypair +@bin bin/antigenic +@bin bin/backtranambig +@bin bin/backtranseq +@bin bin/banana +@bin bin/biosed +@bin bin/btwisted +@bin bin/cai +@bin bin/chaos +@bin bin/charge +@bin bin/checktrans +@bin bin/chips +@bin bin/cirdna +@bin bin/codcmp +@bin bin/codcopy +@bin bin/coderet +@bin bin/compseq +@bin bin/cons +@bin bin/consambig +@bin bin/cpgplot +@bin bin/cpgreport +@bin bin/cusp +@bin bin/cutgextract +@bin bin/cutseq +@bin bin/dan +@bin bin/dbiblast +@bin bin/dbifasta +@bin bin/dbiflat +@bin bin/dbigcg +@bin bin/dbxfasta +@bin bin/dbxflat +@bin bin/dbxgcg +@bin bin/degapseq +@bin bin/density +@bin bin/descseq +@bin bin/diffseq +@bin bin/digest +@bin bin/distmat +@bin bin/dotmatcher +@bin bin/dotpath +@bin bin/dottup +@bin bin/dreg +@bin bin/edialign +@bin bin/einverted +@bin bin/embossdata +@bin bin/embossversion +@bin bin/emma +@bin bin/emowse +@bin bin/entret +@bin bin/epestfind +@bin bin/eprimer3 +@bin bin/equicktandem +@bin bin/est2genome +@bin bin/etandem +@bin bin/extractalign +@bin bin/extractfeat +@bin bin/extractseq +@bin bin/featcopy +@bin bin/featreport +@bin bin/findkm +@bin bin/freak +@bin bin/fuzznuc +@bin bin/fuzzpro +@bin bin/fuzztran +@bin bin/garnier +@bin bin/geecee +@bin bin/getorf +@bin bin/helixturnhelix +@bin bin/hmoment +@bin bin/iep +@bin bin/infoalign +@bin bin/infobase +@bin bin/inforesidue +@bin bin/infoseq +@bin bin/isochore +@bin bin/jaspextract +@bin bin/jaspscan +@bin bin/jembossctl +@bin bin/lindna +@bin bin/listor +@bin bin/makenucseq +@bin bin/makeprotseq +@bin bin/marscan +@bin bin/maskambignuc +@bin bin/maskambigprot +@bin bin/maskfeat +@bin bin/maskseq +@bin bin/matcher +@bin bin/megamerger +@bin bin/merger +@bin bin/msbar +@bin bin/mwcontam +@bin bin/mwfilter +@bin bin/needle +@bin bin/newcpgreport +@bin bin/newcpgseek +@bin bin/newseq +@bin bin/nohtml +@bin bin/noreturn +@bin bin/nospace +@bin bin/notab +@bin bin/notseq +@bin bin/nthseq +@bin bin/octanol +@bin bin/oddcomp +@bin bin/palindrome +@bin bin/pasteseq +@bin bin/patmatdb +@bin bin/patmatmotifs +@bin bin/pepcoil +@bin bin/pepinfo +@bin bin/pepnet +@bin bin/pepstats +@bin bin/pepwheel +@bin bin/pepwindow +@bin bin/pepwindowall +@bin bin/plotcon +@bin bin/plotorf +@bin bin/polydot +@bin bin/preg +@bin bin/prettyplot +@bin bin/prettyseq +@bin bin/primersearch +@bin bin/printsextract +@bin bin/profit +@bin bin/prophecy +@bin bin/prophet +@bin bin/prosextract +@bin bin/pscan +@bin bin/psiphi +@bin bin/rebaseextract +@bin bin/recoder +@bin bin/redata +@bin bin/remap +@bin bin/restover +@bin bin/restrict +@bin bin/revseq bin/runJemboss.csh -bin/seealso -bin/seqmatchall -bin/seqret -bin/seqretsplit -bin/showalign -bin/showdb -bin/showfeat -bin/showorf -bin/showseq -bin/shuffleseq -bin/sigcleave -bin/silent -bin/sirna -bin/sixpack -bin/skipseq -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/twofeat -bin/union -bin/vectorstrip -bin/water -bin/whichdb -bin/wobble -bin/wordcount -bin/wordfinder -bin/wordmatch -bin/wossname -bin/yank +@bin bin/seealso +@bin bin/seqmatchall +@bin bin/seqret +@bin bin/seqretsplit +@bin bin/showalign +@bin bin/showdb +@bin bin/showfeat +@bin bin/showorf +@bin bin/showseq +@bin bin/shuffleseq +@bin bin/sigcleave +@bin bin/silent +@bin bin/sirna +@bin bin/sixpack +@bin bin/sizeseq +@bin bin/skipredundant +@bin bin/skipseq +@bin bin/splitter +@bin bin/stretcher +@bin bin/stssearch +@bin bin/supermatcher +@bin bin/syco +@bin bin/tcode +@bin bin/textsearch +@bin bin/tfextract +@bin bin/tfm +@bin bin/tfscan +@bin bin/tmap +@bin bin/tranalign +@bin bin/transeq +@bin bin/trimest +@bin bin/trimseq +@bin bin/trimspace +@bin bin/twofeat +@bin bin/union +@bin bin/vectorstrip +@bin bin/water +@bin bin/whichdb +@bin bin/wobble +@bin bin/wordcount +@bin bin/wordfinder +@bin bin/wordmatch +@bin bin/wossname +@bin bin/yank include/ajacd.h include/ajalign.h include/ajarch.h @@ -191,6 +209,8 @@ 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 @@ -294,6 +314,8 @@ share/EMBOSS/acd/acdvalid.acd share/EMBOSS/acd/ajbad.acd share/EMBOSS/acd/ajfeatest.acd share/EMBOSS/acd/ajtest.acd +share/EMBOSS/acd/aligncopy.acd +share/EMBOSS/acd/aligncopypair.acd share/EMBOSS/acd/antigenic.acd share/EMBOSS/acd/backtranambig.acd share/EMBOSS/acd/backtranseq.acd @@ -313,6 +335,7 @@ share/EMBOSS/acd/codes.english share/EMBOSS/acd/complex.acd share/EMBOSS/acd/compseq.acd share/EMBOSS/acd/cons.acd +share/EMBOSS/acd/consambig.acd share/EMBOSS/acd/corbatest.acd share/EMBOSS/acd/cpgplot.acd share/EMBOSS/acd/cpgreport.acd @@ -329,14 +352,7 @@ share/EMBOSS/acd/dbxflat.acd share/EMBOSS/acd/dbxgcg.acd share/EMBOSS/acd/dbxstat.acd share/EMBOSS/acd/degapseq.acd -share/EMBOSS/acd/demoalign.acd -share/EMBOSS/acd/demofeatures.acd -share/EMBOSS/acd/demolist.acd -share/EMBOSS/acd/demoreport.acd -share/EMBOSS/acd/demosequence.acd -share/EMBOSS/acd/demostring.acd -share/EMBOSS/acd/demostringnew.acd -share/EMBOSS/acd/demotable.acd +share/EMBOSS/acd/density.acd share/EMBOSS/acd/descseq.acd share/EMBOSS/acd/diffseq.acd share/EMBOSS/acd/digest.acd @@ -361,6 +377,8 @@ share/EMBOSS/acd/etandem.acd share/EMBOSS/acd/extractalign.acd share/EMBOSS/acd/extractfeat.acd share/EMBOSS/acd/extractseq.acd +share/EMBOSS/acd/featcopy.acd +share/EMBOSS/acd/featreport.acd share/EMBOSS/acd/findkm.acd share/EMBOSS/acd/freak.acd share/EMBOSS/acd/fuzznuc.acd @@ -379,6 +397,8 @@ share/EMBOSS/acd/infoalign.acd share/EMBOSS/acd/infoseq.acd share/EMBOSS/acd/intconv.acd share/EMBOSS/acd/isochore.acd +share/EMBOSS/acd/jaspextract.acd +share/EMBOSS/acd/jaspscan.acd share/EMBOSS/acd/keywords.standard share/EMBOSS/acd/knowntypes.standard share/EMBOSS/acd/lindna.acd @@ -386,6 +406,8 @@ share/EMBOSS/acd/listor.acd share/EMBOSS/acd/makenucseq.acd share/EMBOSS/acd/makeprotseq.acd share/EMBOSS/acd/marscan.acd +share/EMBOSS/acd/maskambignuc.acd +share/EMBOSS/acd/maskambigprot.acd share/EMBOSS/acd/maskfeat.acd share/EMBOSS/acd/maskseq.acd share/EMBOSS/acd/matcher.acd @@ -399,7 +421,10 @@ share/EMBOSS/acd/newcoils.acd share/EMBOSS/acd/newcpgreport.acd share/EMBOSS/acd/newcpgseek.acd share/EMBOSS/acd/newseq.acd +share/EMBOSS/acd/nohtml.acd share/EMBOSS/acd/noreturn.acd +share/EMBOSS/acd/nospace.acd +share/EMBOSS/acd/notab.acd share/EMBOSS/acd/notseq.acd share/EMBOSS/acd/nthseq.acd share/EMBOSS/acd/octanol.acd @@ -462,6 +487,8 @@ share/EMBOSS/acd/sigcleave.acd share/EMBOSS/acd/silent.acd share/EMBOSS/acd/sirna.acd share/EMBOSS/acd/sixpack.acd +share/EMBOSS/acd/sizeseq.acd +share/EMBOSS/acd/skipredundant.acd share/EMBOSS/acd/skipseq.acd share/EMBOSS/acd/splitter.acd share/EMBOSS/acd/stretcher.acd @@ -852,6 +879,7 @@ share/EMBOSS/data/Efeatures.embl share/EMBOSS/data/Efeatures.emboss share/EMBOSS/data/Efeatures.gff share/EMBOSS/data/Efeatures.gff3 +share/EMBOSS/data/Efeatures.gff3protein share/EMBOSS/data/Efeatures.gffprotein share/EMBOSS/data/Efeatures.pir share/EMBOSS/data/Efeatures.protein @@ -863,6 +891,7 @@ share/EMBOSS/data/Ehth87.dat share/EMBOSS/data/Emass.dat share/EMBOSS/data/Emassmod.dat share/EMBOSS/data/Ememe.dat +share/EMBOSS/data/Emolwt.dat share/EMBOSS/data/Emwfilter.dat share/EMBOSS/data/Enakai.dat share/EMBOSS/data/Epepcoil.dat @@ -870,6 +899,7 @@ share/EMBOSS/data/Epk.dat share/EMBOSS/data/Epprofile share/EMBOSS/data/Eprior1.plib share/EMBOSS/data/Eprior30.plib +share/EMBOSS/data/Eresidues.iub share/EMBOSS/data/Erna.melt share/EMBOSS/data/Esig.euk share/EMBOSS/data/Esig.pro @@ -884,6 +914,18 @@ share/EMBOSS/data/Etags.swiss share/EMBOSS/data/Etcode.dat share/EMBOSS/data/Evdw.dat share/EMBOSS/data/Ewhite-wimley.dat +share/EMBOSS/data/JASPAR_CNE/ +share/EMBOSS/data/JASPAR_CNE/dummyfile +share/EMBOSS/data/JASPAR_CORE/ +share/EMBOSS/data/JASPAR_CORE/dummyfile +share/EMBOSS/data/JASPAR_FAM/ +share/EMBOSS/data/JASPAR_FAM/dummyfile +share/EMBOSS/data/JASPAR_PHYLOFACTS/ +share/EMBOSS/data/JASPAR_PHYLOFACTS/dummyfile +share/EMBOSS/data/JASPAR_POLII/ +share/EMBOSS/data/JASPAR_POLII/dummyfile +share/EMBOSS/data/JASPAR_SPLICE/ +share/EMBOSS/data/JASPAR_SPLICE/dummyfile share/EMBOSS/data/Matrices.nucleotide share/EMBOSS/data/Matrices.protein share/EMBOSS/data/Matrices.proteinstructure @@ -1235,6 +1277,8 @@ share/EMBOSS/test/data/nuc.pat share/EMBOSS/test/data/nucseq.pat share/EMBOSS/test/data/nucsimple.pat share/EMBOSS/test/data/opsd.msf +share/EMBOSS/test/data/paamir.gff +share/EMBOSS/test/data/paamir.gff3 share/EMBOSS/test/data/paamir.pep share/EMBOSS/test/data/pax6_cdna.fasta share/EMBOSS/test/data/prints.test @@ -1381,260 +1425,6 @@ share/EMBOSS/test/testdb/division.lkp share/EMBOSS/test/testdb/entrynam.idx share/EMBOSS/test/testdb/testdb.fasta share/doc/EMBOSS/ -share/doc/EMBOSS/html/ -share/doc/EMBOSS/html/emboss/ -share/doc/EMBOSS/html/emboss/apps/ -share/doc/EMBOSS/html/emboss/apps/aaindexextract.html -share/doc/EMBOSS/html/emboss/apps/abiview.1.abiview.gif -share/doc/EMBOSS/html/emboss/apps/abiview.html -share/doc/EMBOSS/html/emboss/apps/acd_group.html -share/doc/EMBOSS/html/emboss/apps/acdc.html -share/doc/EMBOSS/html/emboss/apps/acdlog.html -share/doc/EMBOSS/html/emboss/apps/acdpretty.html -share/doc/EMBOSS/html/emboss/apps/acdtable.html -share/doc/EMBOSS/html/emboss/apps/acdtrace.html -share/doc/EMBOSS/html/emboss/apps/acdvalid.html -share/doc/EMBOSS/html/emboss/apps/ajtest.html -share/doc/EMBOSS/html/emboss/apps/alignment_consensus_group.html -share/doc/EMBOSS/html/emboss/apps/alignment_differences_group.html -share/doc/EMBOSS/html/emboss/apps/alignment_dot_plots_group.html -share/doc/EMBOSS/html/emboss/apps/alignment_global_group.html -share/doc/EMBOSS/html/emboss/apps/alignment_local_group.html -share/doc/EMBOSS/html/emboss/apps/alignment_multiple_group.html -share/doc/EMBOSS/html/emboss/apps/antigenic.html -share/doc/EMBOSS/html/emboss/apps/backtranambig.html -share/doc/EMBOSS/html/emboss/apps/backtranseq.html -share/doc/EMBOSS/html/emboss/apps/banana.1.banana.gif -share/doc/EMBOSS/html/emboss/apps/banana.html -share/doc/EMBOSS/html/emboss/apps/biosed.html -share/doc/EMBOSS/html/emboss/apps/btwisted.html -share/doc/EMBOSS/html/emboss/apps/cai.html -share/doc/EMBOSS/html/emboss/apps/chaos.1.chaos.gif -share/doc/EMBOSS/html/emboss/apps/chaos.html -share/doc/EMBOSS/html/emboss/apps/charge.html -share/doc/EMBOSS/html/emboss/apps/checktrans.html -share/doc/EMBOSS/html/emboss/apps/chips.html -share/doc/EMBOSS/html/emboss/apps/cirdna.1.cirdna.gif -share/doc/EMBOSS/html/emboss/apps/cirdna.html -share/doc/EMBOSS/html/emboss/apps/codcmp.html -share/doc/EMBOSS/html/emboss/apps/codcopy.html -share/doc/EMBOSS/html/emboss/apps/coderet.html -share/doc/EMBOSS/html/emboss/apps/compseq.html -share/doc/EMBOSS/html/emboss/apps/cons.html -share/doc/EMBOSS/html/emboss/apps/cpgplot.1.cpgplot.gif -share/doc/EMBOSS/html/emboss/apps/cpgplot.html -share/doc/EMBOSS/html/emboss/apps/cpgreport.html -share/doc/EMBOSS/html/emboss/apps/cusp.html -share/doc/EMBOSS/html/emboss/apps/cutgextract.html -share/doc/EMBOSS/html/emboss/apps/cutseq.html -share/doc/EMBOSS/html/emboss/apps/dan.2.dan.gif -share/doc/EMBOSS/html/emboss/apps/dan.html -share/doc/EMBOSS/html/emboss/apps/dbiblast.html -share/doc/EMBOSS/html/emboss/apps/dbifasta.html -share/doc/EMBOSS/html/emboss/apps/dbiflat.html -share/doc/EMBOSS/html/emboss/apps/dbigcg.html -share/doc/EMBOSS/html/emboss/apps/dbxfasta.html -share/doc/EMBOSS/html/emboss/apps/dbxflat.html -share/doc/EMBOSS/html/emboss/apps/dbxgcg.html -share/doc/EMBOSS/html/emboss/apps/degapseq.html -share/doc/EMBOSS/html/emboss/apps/descseq.html -share/doc/EMBOSS/html/emboss/apps/diffseq.html -share/doc/EMBOSS/html/emboss/apps/digest.html -share/doc/EMBOSS/html/emboss/apps/display_group.html -share/doc/EMBOSS/html/emboss/apps/distmat.html -share/doc/EMBOSS/html/emboss/apps/dotmatcher.1.dotmatcher.gif -share/doc/EMBOSS/html/emboss/apps/dotmatcher.html -share/doc/EMBOSS/html/emboss/apps/dotpath.1.dotpath.gif -share/doc/EMBOSS/html/emboss/apps/dotpath.html -share/doc/EMBOSS/html/emboss/apps/dottup.1.dottup.gif -share/doc/EMBOSS/html/emboss/apps/dottup.html -share/doc/EMBOSS/html/emboss/apps/dreg.html -share/doc/EMBOSS/html/emboss/apps/edialign.html -share/doc/EMBOSS/html/emboss/apps/einverted.html -share/doc/EMBOSS/html/emboss/apps/emboss_icon.gif -share/doc/EMBOSS/html/emboss/apps/emboss_icon.jpg -share/doc/EMBOSS/html/emboss/apps/embossdata.html -share/doc/EMBOSS/html/emboss/apps/embossversion.html -share/doc/EMBOSS/html/emboss/apps/emma.html -share/doc/EMBOSS/html/emboss/apps/emowse.html -share/doc/EMBOSS/html/emboss/apps/entret.html -share/doc/EMBOSS/html/emboss/apps/enzyme_kinetics_group.html -share/doc/EMBOSS/html/emboss/apps/epestfind.html -share/doc/EMBOSS/html/emboss/apps/eprimer3.html -share/doc/EMBOSS/html/emboss/apps/equicktandem.html -share/doc/EMBOSS/html/emboss/apps/est2genome.html -share/doc/EMBOSS/html/emboss/apps/etandem.html -share/doc/EMBOSS/html/emboss/apps/extractfeat.html -share/doc/EMBOSS/html/emboss/apps/extractseq.html -share/doc/EMBOSS/html/emboss/apps/feature_tables_group.html -share/doc/EMBOSS/html/emboss/apps/findkm.1.findkm.gif -share/doc/EMBOSS/html/emboss/apps/findkm.html -share/doc/EMBOSS/html/emboss/apps/freak.html -share/doc/EMBOSS/html/emboss/apps/fuzznuc.html -share/doc/EMBOSS/html/emboss/apps/fuzzpro.html -share/doc/EMBOSS/html/emboss/apps/fuzztran.html -share/doc/EMBOSS/html/emboss/apps/garnier.html -share/doc/EMBOSS/html/emboss/apps/geecee.html -share/doc/EMBOSS/html/emboss/apps/getorf.html -share/doc/EMBOSS/html/emboss/apps/groups.html -share/doc/EMBOSS/html/emboss/apps/helixturnhelix.html -share/doc/EMBOSS/html/emboss/apps/hmm_group.html -share/doc/EMBOSS/html/emboss/apps/hmoment.html -share/doc/EMBOSS/html/emboss/apps/iep.html -share/doc/EMBOSS/html/emboss/apps/index.html -share/doc/EMBOSS/html/emboss/apps/infoalign.html -share/doc/EMBOSS/html/emboss/apps/information_group.html -share/doc/EMBOSS/html/emboss/apps/infoseq.html -share/doc/EMBOSS/html/emboss/apps/isochore.1.isochore.gif -share/doc/EMBOSS/html/emboss/apps/isochore.html -share/doc/EMBOSS/html/emboss/apps/jembossctl.html -share/doc/EMBOSS/html/emboss/apps/lindna.1.lindna.gif -share/doc/EMBOSS/html/emboss/apps/lindna.html -share/doc/EMBOSS/html/emboss/apps/listor.html -share/doc/EMBOSS/html/emboss/apps/makenucseq.html -share/doc/EMBOSS/html/emboss/apps/makeprotseq.html -share/doc/EMBOSS/html/emboss/apps/marscan.html -share/doc/EMBOSS/html/emboss/apps/maskfeat.html -share/doc/EMBOSS/html/emboss/apps/maskseq.html -share/doc/EMBOSS/html/emboss/apps/matcher.html -share/doc/EMBOSS/html/emboss/apps/megamerger.html -share/doc/EMBOSS/html/emboss/apps/menus_group.html -share/doc/EMBOSS/html/emboss/apps/merger.html -share/doc/EMBOSS/html/emboss/apps/msbar.html -share/doc/EMBOSS/html/emboss/apps/mwcontam.html -share/doc/EMBOSS/html/emboss/apps/mwfilter.html -share/doc/EMBOSS/html/emboss/apps/needle.html -share/doc/EMBOSS/html/emboss/apps/newcpgreport.html -share/doc/EMBOSS/html/emboss/apps/newcpgseek.html -share/doc/EMBOSS/html/emboss/apps/newseq.html -share/doc/EMBOSS/html/emboss/apps/noreturn.html -share/doc/EMBOSS/html/emboss/apps/notseq.html -share/doc/EMBOSS/html/emboss/apps/nthseq.html -share/doc/EMBOSS/html/emboss/apps/nucleic_2d_structure_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_codon_usage_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_codon_usage_nucleic_gene_finding_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_composition_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_cpg_islands_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_gene_finding_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_motifs_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_mutation_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_primers_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_profiles_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_repeats_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_restriction_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_transcription_group.html -share/doc/EMBOSS/html/emboss/apps/nucleic_translation_group.html -share/doc/EMBOSS/html/emboss/apps/octanol.1.octanol.gif -share/doc/EMBOSS/html/emboss/apps/octanol.html -share/doc/EMBOSS/html/emboss/apps/oddcomp.html -share/doc/EMBOSS/html/emboss/apps/palindrome.html -share/doc/EMBOSS/html/emboss/apps/pasteseq.html -share/doc/EMBOSS/html/emboss/apps/patmatdb.html -share/doc/EMBOSS/html/emboss/apps/patmatmotifs.html -share/doc/EMBOSS/html/emboss/apps/pepcoil.html -share/doc/EMBOSS/html/emboss/apps/pepinfo.1.pepinfo.gif -share/doc/EMBOSS/html/emboss/apps/pepinfo.html -share/doc/EMBOSS/html/emboss/apps/pepnet.1.pepnet.gif -share/doc/EMBOSS/html/emboss/apps/pepnet.html -share/doc/EMBOSS/html/emboss/apps/pepstats.html -share/doc/EMBOSS/html/emboss/apps/pepwheel.1.pepwheel.gif -share/doc/EMBOSS/html/emboss/apps/pepwheel.html -share/doc/EMBOSS/html/emboss/apps/pepwindow.1.pepwindow.gif -share/doc/EMBOSS/html/emboss/apps/pepwindow.html -share/doc/EMBOSS/html/emboss/apps/pepwindowall.1.pepwindowall.gif -share/doc/EMBOSS/html/emboss/apps/pepwindowall.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_consensus_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_continuous_characters_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_discrete_characters_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_distance_matrix_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_gene_frequencies_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_molecular_sequence_group.html -share/doc/EMBOSS/html/emboss/apps/phylogeny_tree_drawing_group.html -share/doc/EMBOSS/html/emboss/apps/plotcon.1.plotcon.gif -share/doc/EMBOSS/html/emboss/apps/plotcon.html -share/doc/EMBOSS/html/emboss/apps/plotorf.1.plotorf.gif -share/doc/EMBOSS/html/emboss/apps/plotorf.2.plotorf.gif -share/doc/EMBOSS/html/emboss/apps/plotorf.html -share/doc/EMBOSS/html/emboss/apps/polydot.1.polydot.gif -share/doc/EMBOSS/html/emboss/apps/polydot.html -share/doc/EMBOSS/html/emboss/apps/preg.html -share/doc/EMBOSS/html/emboss/apps/prettyplot.1.prettyplot.gif -share/doc/EMBOSS/html/emboss/apps/prettyplot.2.prettyplot.gif -share/doc/EMBOSS/html/emboss/apps/prettyplot.html -share/doc/EMBOSS/html/emboss/apps/prettyseq.html -share/doc/EMBOSS/html/emboss/apps/primersearch.html -share/doc/EMBOSS/html/emboss/apps/printsextract.html -share/doc/EMBOSS/html/emboss/apps/profit.html -share/doc/EMBOSS/html/emboss/apps/prophecy.html -share/doc/EMBOSS/html/emboss/apps/prophet.html -share/doc/EMBOSS/html/emboss/apps/prosextract.html -share/doc/EMBOSS/html/emboss/apps/protein_2d_structure_group.html -share/doc/EMBOSS/html/emboss/apps/protein_3d_structure_group.html -share/doc/EMBOSS/html/emboss/apps/protein_composition_group.html -share/doc/EMBOSS/html/emboss/apps/protein_motifs_group.html -share/doc/EMBOSS/html/emboss/apps/protein_mutation_group.html -share/doc/EMBOSS/html/emboss/apps/protein_profiles_group.html -share/doc/EMBOSS/html/emboss/apps/protein_sequence_alignment_group.html -share/doc/EMBOSS/html/emboss/apps/pscan.html -share/doc/EMBOSS/html/emboss/apps/psiphi.html -share/doc/EMBOSS/html/emboss/apps/rebaseextract.html -share/doc/EMBOSS/html/emboss/apps/recoder.html -share/doc/EMBOSS/html/emboss/apps/redata.html -share/doc/EMBOSS/html/emboss/apps/remap.html -share/doc/EMBOSS/html/emboss/apps/restover.html -share/doc/EMBOSS/html/emboss/apps/restrict.html -share/doc/EMBOSS/html/emboss/apps/revseq.html -share/doc/EMBOSS/html/emboss/apps/seealso.html -share/doc/EMBOSS/html/emboss/apps/seqmatchall.html -share/doc/EMBOSS/html/emboss/apps/seqret.html -share/doc/EMBOSS/html/emboss/apps/seqretsplit.html -share/doc/EMBOSS/html/emboss/apps/showalign.html -share/doc/EMBOSS/html/emboss/apps/showdb.html -share/doc/EMBOSS/html/emboss/apps/showfeat.html -share/doc/EMBOSS/html/emboss/apps/showorf.html -share/doc/EMBOSS/html/emboss/apps/showseq.html -share/doc/EMBOSS/html/emboss/apps/shuffleseq.html -share/doc/EMBOSS/html/emboss/apps/sigcleave.html -share/doc/EMBOSS/html/emboss/apps/silent.html -share/doc/EMBOSS/html/emboss/apps/sirna.html -share/doc/EMBOSS/html/emboss/apps/sixpack.html -share/doc/EMBOSS/html/emboss/apps/skipseq.html -share/doc/EMBOSS/html/emboss/apps/splitter.html -share/doc/EMBOSS/html/emboss/apps/stretcher.html -share/doc/EMBOSS/html/emboss/apps/stssearch.html -share/doc/EMBOSS/html/emboss/apps/supermatcher.html -share/doc/EMBOSS/html/emboss/apps/syco.1.syco.gif -share/doc/EMBOSS/html/emboss/apps/syco.html -share/doc/EMBOSS/html/emboss/apps/tcode.2.tcode.gif -share/doc/EMBOSS/html/emboss/apps/tcode.html -share/doc/EMBOSS/html/emboss/apps/template.html -share/doc/EMBOSS/html/emboss/apps/test_group.html -share/doc/EMBOSS/html/emboss/apps/textsearch.html -share/doc/EMBOSS/html/emboss/apps/tfextract.html -share/doc/EMBOSS/html/emboss/apps/tfm.html -share/doc/EMBOSS/html/emboss/apps/tfscan.html -share/doc/EMBOSS/html/emboss/apps/tmap.1.tmap.gif -share/doc/EMBOSS/html/emboss/apps/tmap.html -share/doc/EMBOSS/html/emboss/apps/tranalign.html -share/doc/EMBOSS/html/emboss/apps/transeq.html -share/doc/EMBOSS/html/emboss/apps/trimest.html -share/doc/EMBOSS/html/emboss/apps/trimseq.html -share/doc/EMBOSS/html/emboss/apps/twofeat.html -share/doc/EMBOSS/html/emboss/apps/union.html -share/doc/EMBOSS/html/emboss/apps/utils_database_creation_group.html -share/doc/EMBOSS/html/emboss/apps/utils_database_indexing_group.html -share/doc/EMBOSS/html/emboss/apps/utils_misc_group.html -share/doc/EMBOSS/html/emboss/apps/vectorstrip.html -share/doc/EMBOSS/html/emboss/apps/water.html -share/doc/EMBOSS/html/emboss/apps/whichdb.html -share/doc/EMBOSS/html/emboss/apps/wobble.1.wobble.gif -share/doc/EMBOSS/html/emboss/apps/wobble.html -share/doc/EMBOSS/html/emboss/apps/wordcount.html -share/doc/EMBOSS/html/emboss/apps/wordfinder.html -share/doc/EMBOSS/html/emboss/apps/wordmatch.html -share/doc/EMBOSS/html/emboss/apps/wossname.html -share/doc/EMBOSS/html/emboss/apps/yank.html share/doc/EMBOSS/manuals/ share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt share/doc/EMBOSS/manuals/admin.aux @@ -1652,6 +1442,283 @@ share/doc/EMBOSS/manuals/emboss_qg.ps share/doc/EMBOSS/manuals/fdl.txt share/doc/EMBOSS/manuals/program.ps.gz share/doc/EMBOSS/programs/ +share/doc/EMBOSS/programs/html/ +share/doc/EMBOSS/programs/html/aaindexextract.html +share/doc/EMBOSS/programs/html/abiview.1.abiview.gif +share/doc/EMBOSS/programs/html/abiview.html +share/doc/EMBOSS/programs/html/acd_group.html +share/doc/EMBOSS/programs/html/acdc.html +share/doc/EMBOSS/programs/html/acdlog.html +share/doc/EMBOSS/programs/html/acdpretty.html +share/doc/EMBOSS/programs/html/acdtable.html +share/doc/EMBOSS/programs/html/acdtrace.html +share/doc/EMBOSS/programs/html/acdvalid.html +share/doc/EMBOSS/programs/html/ajtest.html +share/doc/EMBOSS/programs/html/aligncopy.html +share/doc/EMBOSS/programs/html/aligncopypair.html +share/doc/EMBOSS/programs/html/alignment_consensus_group.html +share/doc/EMBOSS/programs/html/alignment_differences_group.html +share/doc/EMBOSS/programs/html/alignment_dot_plots_group.html +share/doc/EMBOSS/programs/html/alignment_global_group.html +share/doc/EMBOSS/programs/html/alignment_local_group.html +share/doc/EMBOSS/programs/html/alignment_multiple_group.html +share/doc/EMBOSS/programs/html/antigenic.html +share/doc/EMBOSS/programs/html/assembly_fragment_assembly_group.html +share/doc/EMBOSS/programs/html/backtranambig.html +share/doc/EMBOSS/programs/html/backtranseq.html +share/doc/EMBOSS/programs/html/banana.1.banana.gif +share/doc/EMBOSS/programs/html/banana.html +share/doc/EMBOSS/programs/html/biosed.html +share/doc/EMBOSS/programs/html/btwisted.html +share/doc/EMBOSS/programs/html/cai.html +share/doc/EMBOSS/programs/html/chaos.1.chaos.gif +share/doc/EMBOSS/programs/html/chaos.html +share/doc/EMBOSS/programs/html/charge.html +share/doc/EMBOSS/programs/html/checktrans.html +share/doc/EMBOSS/programs/html/chips.html +share/doc/EMBOSS/programs/html/cirdna.1.cirdna.gif +share/doc/EMBOSS/programs/html/cirdna.html +share/doc/EMBOSS/programs/html/codcmp.html +share/doc/EMBOSS/programs/html/codcopy.html +share/doc/EMBOSS/programs/html/coderet.html +share/doc/EMBOSS/programs/html/complex.html +share/doc/EMBOSS/programs/html/compseq.html +share/doc/EMBOSS/programs/html/cons.html +share/doc/EMBOSS/programs/html/consambig.html +share/doc/EMBOSS/programs/html/cpgplot.1.cpgplot.gif +share/doc/EMBOSS/programs/html/cpgplot.html +share/doc/EMBOSS/programs/html/cpgreport.html +share/doc/EMBOSS/programs/html/cusp.html +share/doc/EMBOSS/programs/html/cutgextract.html +share/doc/EMBOSS/programs/html/cutseq.html +share/doc/EMBOSS/programs/html/dan.2.dan.gif +share/doc/EMBOSS/programs/html/dan.html +share/doc/EMBOSS/programs/html/dbiblast.html +share/doc/EMBOSS/programs/html/dbifasta.html +share/doc/EMBOSS/programs/html/dbiflat.html +share/doc/EMBOSS/programs/html/dbigcg.html +share/doc/EMBOSS/programs/html/dbxfasta.html +share/doc/EMBOSS/programs/html/dbxflat.html +share/doc/EMBOSS/programs/html/dbxgcg.html +share/doc/EMBOSS/programs/html/degapseq.html +share/doc/EMBOSS/programs/html/density.html +share/doc/EMBOSS/programs/html/descseq.html +share/doc/EMBOSS/programs/html/diffseq.html +share/doc/EMBOSS/programs/html/digest.html +share/doc/EMBOSS/programs/html/display_group.html +share/doc/EMBOSS/programs/html/distmat.html +share/doc/EMBOSS/programs/html/dotmatcher.1.dotmatcher.gif +share/doc/EMBOSS/programs/html/dotmatcher.html +share/doc/EMBOSS/programs/html/dotpath.1.dotpath.gif +share/doc/EMBOSS/programs/html/dotpath.html +share/doc/EMBOSS/programs/html/dottup.1.dottup.gif +share/doc/EMBOSS/programs/html/dottup.html +share/doc/EMBOSS/programs/html/dreg.html +share/doc/EMBOSS/programs/html/edialign.html +share/doc/EMBOSS/programs/html/edit_group.html +share/doc/EMBOSS/programs/html/einverted.html +share/doc/EMBOSS/programs/html/emboss_icon.gif +share/doc/EMBOSS/programs/html/emboss_icon.jpg +share/doc/EMBOSS/programs/html/embossdata.html +share/doc/EMBOSS/programs/html/embossversion.html +share/doc/EMBOSS/programs/html/emma.html +share/doc/EMBOSS/programs/html/emowse.html +share/doc/EMBOSS/programs/html/entret.html +share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html +share/doc/EMBOSS/programs/html/epestfind.1.epestfind.gif +share/doc/EMBOSS/programs/html/epestfind.html +share/doc/EMBOSS/programs/html/eprimer3.html +share/doc/EMBOSS/programs/html/equicktandem.html +share/doc/EMBOSS/programs/html/est2genome.html +share/doc/EMBOSS/programs/html/etandem.html +share/doc/EMBOSS/programs/html/extractalign.html +share/doc/EMBOSS/programs/html/extractfeat.html +share/doc/EMBOSS/programs/html/extractseq.html +share/doc/EMBOSS/programs/html/featcopy.html +share/doc/EMBOSS/programs/html/featreport.html +share/doc/EMBOSS/programs/html/feature_tables_group.html +share/doc/EMBOSS/programs/html/findkm.1.findkm.gif +share/doc/EMBOSS/programs/html/findkm.html +share/doc/EMBOSS/programs/html/freak.html +share/doc/EMBOSS/programs/html/fuzznuc.html +share/doc/EMBOSS/programs/html/fuzzpro.html +share/doc/EMBOSS/programs/html/fuzztran.html +share/doc/EMBOSS/programs/html/garnier.html +share/doc/EMBOSS/programs/html/geecee.html +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/hmm_group.html +share/doc/EMBOSS/programs/html/hmoment.html +share/doc/EMBOSS/programs/html/iep.html +share/doc/EMBOSS/programs/html/index.html +share/doc/EMBOSS/programs/html/infoalign.html +share/doc/EMBOSS/programs/html/infobase.html +share/doc/EMBOSS/programs/html/inforesidue.html +share/doc/EMBOSS/programs/html/information_group.html +share/doc/EMBOSS/programs/html/infoseq.html +share/doc/EMBOSS/programs/html/isochore.1.isochore.gif +share/doc/EMBOSS/programs/html/isochore.html +share/doc/EMBOSS/programs/html/jaspextract.html +share/doc/EMBOSS/programs/html/jaspscan.html +share/doc/EMBOSS/programs/html/jembossctl.html +share/doc/EMBOSS/programs/html/libscan.html +share/doc/EMBOSS/programs/html/lindna.1.lindna.gif +share/doc/EMBOSS/programs/html/lindna.html +share/doc/EMBOSS/programs/html/listor.html +share/doc/EMBOSS/programs/html/makenucseq.html +share/doc/EMBOSS/programs/html/makeprotseq.html +share/doc/EMBOSS/programs/html/marscan.html +share/doc/EMBOSS/programs/html/maskambignuc.html +share/doc/EMBOSS/programs/html/maskambigprot.html +share/doc/EMBOSS/programs/html/maskfeat.html +share/doc/EMBOSS/programs/html/maskseq.html +share/doc/EMBOSS/programs/html/matcher.html +share/doc/EMBOSS/programs/html/megamerger.html +share/doc/EMBOSS/programs/html/menus_group.html +share/doc/EMBOSS/programs/html/merger.html +share/doc/EMBOSS/programs/html/msbar.html +share/doc/EMBOSS/programs/html/mwcontam.html +share/doc/EMBOSS/programs/html/mwfilter.html +share/doc/EMBOSS/programs/html/needle.html +share/doc/EMBOSS/programs/html/newcpgreport.html +share/doc/EMBOSS/programs/html/newcpgseek.html +share/doc/EMBOSS/programs/html/newseq.html +share/doc/EMBOSS/programs/html/nohtml.html +share/doc/EMBOSS/programs/html/noreturn.html +share/doc/EMBOSS/programs/html/nospace.html +share/doc/EMBOSS/programs/html/notab.html +share/doc/EMBOSS/programs/html/notseq.html +share/doc/EMBOSS/programs/html/nthseq.html +share/doc/EMBOSS/programs/html/nucleic_2d_structure_group.html +share/doc/EMBOSS/programs/html/nucleic_codon_usage_group.html +share/doc/EMBOSS/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html +share/doc/EMBOSS/programs/html/nucleic_composition_group.html +share/doc/EMBOSS/programs/html/nucleic_cpg_islands_group.html +share/doc/EMBOSS/programs/html/nucleic_gene_finding_group.html +share/doc/EMBOSS/programs/html/nucleic_motifs_group.html +share/doc/EMBOSS/programs/html/nucleic_mutation_group.html +share/doc/EMBOSS/programs/html/nucleic_primers_group.html +share/doc/EMBOSS/programs/html/nucleic_profiles_group.html +share/doc/EMBOSS/programs/html/nucleic_repeats_group.html +share/doc/EMBOSS/programs/html/nucleic_restriction_group.html +share/doc/EMBOSS/programs/html/nucleic_rna_folding_group.html +share/doc/EMBOSS/programs/html/nucleic_transcription_group.html +share/doc/EMBOSS/programs/html/nucleic_translation_group.html +share/doc/EMBOSS/programs/html/octanol.1.octanol.gif +share/doc/EMBOSS/programs/html/octanol.html +share/doc/EMBOSS/programs/html/oddcomp.html +share/doc/EMBOSS/programs/html/palindrome.html +share/doc/EMBOSS/programs/html/pasteseq.html +share/doc/EMBOSS/programs/html/patmatdb.html +share/doc/EMBOSS/programs/html/patmatmotifs.html +share/doc/EMBOSS/programs/html/pepcoil.html +share/doc/EMBOSS/programs/html/pepinfo.1.pepinfo.gif +share/doc/EMBOSS/programs/html/pepinfo.html +share/doc/EMBOSS/programs/html/pepnet.1.pepnet.gif +share/doc/EMBOSS/programs/html/pepnet.html +share/doc/EMBOSS/programs/html/pepstats.html +share/doc/EMBOSS/programs/html/pepwheel.1.pepwheel.gif +share/doc/EMBOSS/programs/html/pepwheel.html +share/doc/EMBOSS/programs/html/pepwindow.1.pepwindow.gif +share/doc/EMBOSS/programs/html/pepwindow.html +share/doc/EMBOSS/programs/html/pepwindowall.1.pepwindowall.gif +share/doc/EMBOSS/programs/html/pepwindowall.html +share/doc/EMBOSS/programs/html/phylogeny_consensus_group.html +share/doc/EMBOSS/programs/html/phylogeny_continuous_characters_group.html +share/doc/EMBOSS/programs/html/phylogeny_discrete_characters_group.html +share/doc/EMBOSS/programs/html/phylogeny_distance_matrix_group.html +share/doc/EMBOSS/programs/html/phylogeny_gene_frequencies_group.html +share/doc/EMBOSS/programs/html/phylogeny_group.html +share/doc/EMBOSS/programs/html/phylogeny_molecular_sequence_group.html +share/doc/EMBOSS/programs/html/phylogeny_tree_drawing_group.html +share/doc/EMBOSS/programs/html/plotcon.1.plotcon.gif +share/doc/EMBOSS/programs/html/plotcon.html +share/doc/EMBOSS/programs/html/plotorf.1.plotorf.gif +share/doc/EMBOSS/programs/html/plotorf.2.plotorf.gif +share/doc/EMBOSS/programs/html/plotorf.html +share/doc/EMBOSS/programs/html/polydot.1.polydot.gif +share/doc/EMBOSS/programs/html/polydot.html +share/doc/EMBOSS/programs/html/preg.html +share/doc/EMBOSS/programs/html/prettyplot.1.prettyplot.gif +share/doc/EMBOSS/programs/html/prettyplot.2.prettyplot.gif +share/doc/EMBOSS/programs/html/prettyplot.html +share/doc/EMBOSS/programs/html/prettyseq.html +share/doc/EMBOSS/programs/html/primersearch.html +share/doc/EMBOSS/programs/html/printsextract.html +share/doc/EMBOSS/programs/html/profit.html +share/doc/EMBOSS/programs/html/prophecy.html +share/doc/EMBOSS/programs/html/prophet.html +share/doc/EMBOSS/programs/html/prosextract.html +share/doc/EMBOSS/programs/html/protein_2d_structure_group.html +share/doc/EMBOSS/programs/html/protein_3d_structure_group.html +share/doc/EMBOSS/programs/html/protein_composition_group.html +share/doc/EMBOSS/programs/html/protein_motifs_group.html +share/doc/EMBOSS/programs/html/protein_mutation_group.html +share/doc/EMBOSS/programs/html/protein_profiles_group.html +share/doc/EMBOSS/programs/html/protein_sequence_alignment_group.html +share/doc/EMBOSS/programs/html/pscan.html +share/doc/EMBOSS/programs/html/psiphi.html +share/doc/EMBOSS/programs/html/rebaseextract.html +share/doc/EMBOSS/programs/html/recoder.html +share/doc/EMBOSS/programs/html/redata.html +share/doc/EMBOSS/programs/html/remap.html +share/doc/EMBOSS/programs/html/restover.html +share/doc/EMBOSS/programs/html/restrict.html +share/doc/EMBOSS/programs/html/revseq.html +share/doc/EMBOSS/programs/html/seealso.html +share/doc/EMBOSS/programs/html/seqmatchall.html +share/doc/EMBOSS/programs/html/seqret.html +share/doc/EMBOSS/programs/html/seqretsplit.html +share/doc/EMBOSS/programs/html/showalign.html +share/doc/EMBOSS/programs/html/showdb.html +share/doc/EMBOSS/programs/html/showfeat.html +share/doc/EMBOSS/programs/html/showorf.html +share/doc/EMBOSS/programs/html/showseq.html +share/doc/EMBOSS/programs/html/shuffleseq.html +share/doc/EMBOSS/programs/html/sigcleave.html +share/doc/EMBOSS/programs/html/silent.html +share/doc/EMBOSS/programs/html/sirna.html +share/doc/EMBOSS/programs/html/sixpack.html +share/doc/EMBOSS/programs/html/sizeseq.html +share/doc/EMBOSS/programs/html/skipredundant.html +share/doc/EMBOSS/programs/html/skipseq.html +share/doc/EMBOSS/programs/html/splitter.html +share/doc/EMBOSS/programs/html/stretcher.html +share/doc/EMBOSS/programs/html/stssearch.html +share/doc/EMBOSS/programs/html/supermatcher.html +share/doc/EMBOSS/programs/html/syco.1.syco.gif +share/doc/EMBOSS/programs/html/syco.html +share/doc/EMBOSS/programs/html/tcode.2.tcode.gif +share/doc/EMBOSS/programs/html/tcode.html +share/doc/EMBOSS/programs/html/template.html +share/doc/EMBOSS/programs/html/test_group.html +share/doc/EMBOSS/programs/html/textsearch.html +share/doc/EMBOSS/programs/html/tfextract.html +share/doc/EMBOSS/programs/html/tfm.html +share/doc/EMBOSS/programs/html/tfscan.html +share/doc/EMBOSS/programs/html/tmap.1.tmap.gif +share/doc/EMBOSS/programs/html/tmap.html +share/doc/EMBOSS/programs/html/tranalign.html +share/doc/EMBOSS/programs/html/transeq.html +share/doc/EMBOSS/programs/html/trimest.html +share/doc/EMBOSS/programs/html/trimseq.html +share/doc/EMBOSS/programs/html/trimspace.html +share/doc/EMBOSS/programs/html/twofeat.html +share/doc/EMBOSS/programs/html/union.html +share/doc/EMBOSS/programs/html/utils_database_creation_group.html +share/doc/EMBOSS/programs/html/utils_database_indexing_group.html +share/doc/EMBOSS/programs/html/utils_misc_group.html +share/doc/EMBOSS/programs/html/vectorstrip.html +share/doc/EMBOSS/programs/html/water.html +share/doc/EMBOSS/programs/html/whichdb.html +share/doc/EMBOSS/programs/html/wobble.1.wobble.gif +share/doc/EMBOSS/programs/html/wobble.html +share/doc/EMBOSS/programs/html/wordcount.html +share/doc/EMBOSS/programs/html/wordfinder.html +share/doc/EMBOSS/programs/html/wordmatch.html +share/doc/EMBOSS/programs/html/wossname.html +share/doc/EMBOSS/programs/html/yank.html share/doc/EMBOSS/programs/text/ share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt share/doc/EMBOSS/programs/text/aaindexextract.txt @@ -1662,6 +1729,8 @@ share/doc/EMBOSS/programs/text/acdpretty.txt share/doc/EMBOSS/programs/text/acdtable.txt share/doc/EMBOSS/programs/text/acdtrace.txt share/doc/EMBOSS/programs/text/acdvalid.txt +share/doc/EMBOSS/programs/text/aligncopy.txt +share/doc/EMBOSS/programs/text/aligncopypair.txt share/doc/EMBOSS/programs/text/antigenic.txt share/doc/EMBOSS/programs/text/backtranambig.txt share/doc/EMBOSS/programs/text/backtranseq.txt @@ -1680,6 +1749,7 @@ share/doc/EMBOSS/programs/text/coderet.txt share/doc/EMBOSS/programs/text/complex.txt share/doc/EMBOSS/programs/text/compseq.txt share/doc/EMBOSS/programs/text/cons.txt +share/doc/EMBOSS/programs/text/consambig.txt share/doc/EMBOSS/programs/text/cpgplot.txt share/doc/EMBOSS/programs/text/cpgreport.txt share/doc/EMBOSS/programs/text/cusp.txt @@ -1694,6 +1764,7 @@ share/doc/EMBOSS/programs/text/dbxfasta.txt share/doc/EMBOSS/programs/text/dbxflat.txt share/doc/EMBOSS/programs/text/dbxgcg.txt share/doc/EMBOSS/programs/text/degapseq.txt +share/doc/EMBOSS/programs/text/density.txt share/doc/EMBOSS/programs/text/descseq.txt share/doc/EMBOSS/programs/text/diffseq.txt share/doc/EMBOSS/programs/text/digest.txt @@ -1714,10 +1785,14 @@ share/doc/EMBOSS/programs/text/eprimer3.txt share/doc/EMBOSS/programs/text/equicktandem.txt share/doc/EMBOSS/programs/text/est2genome.txt share/doc/EMBOSS/programs/text/etandem.txt +share/doc/EMBOSS/programs/text/extractalign.txt share/doc/EMBOSS/programs/text/extractfeat.txt share/doc/EMBOSS/programs/text/extractseq.txt +share/doc/EMBOSS/programs/text/featcopy.txt +share/doc/EMBOSS/programs/text/featreport.txt share/doc/EMBOSS/programs/text/findkm.txt share/doc/EMBOSS/programs/text/freak.txt +share/doc/EMBOSS/programs/text/frestdist.txt share/doc/EMBOSS/programs/text/fuzznuc.txt share/doc/EMBOSS/programs/text/fuzzpro.txt share/doc/EMBOSS/programs/text/fuzztran.txt @@ -1728,14 +1803,20 @@ share/doc/EMBOSS/programs/text/helixturnhelix.txt share/doc/EMBOSS/programs/text/hmoment.txt share/doc/EMBOSS/programs/text/iep.txt share/doc/EMBOSS/programs/text/infoalign.txt +share/doc/EMBOSS/programs/text/infobase.txt +share/doc/EMBOSS/programs/text/inforesidue.txt share/doc/EMBOSS/programs/text/infoseq.txt share/doc/EMBOSS/programs/text/isochore.txt +share/doc/EMBOSS/programs/text/jaspextract.txt +share/doc/EMBOSS/programs/text/jaspscan.txt share/doc/EMBOSS/programs/text/jembossctl.txt share/doc/EMBOSS/programs/text/lindna.txt share/doc/EMBOSS/programs/text/listor.txt share/doc/EMBOSS/programs/text/makenucseq.txt share/doc/EMBOSS/programs/text/makeprotseq.txt share/doc/EMBOSS/programs/text/marscan.txt +share/doc/EMBOSS/programs/text/maskambignuc.txt +share/doc/EMBOSS/programs/text/maskambigprot.txt share/doc/EMBOSS/programs/text/maskfeat.txt share/doc/EMBOSS/programs/text/maskseq.txt share/doc/EMBOSS/programs/text/matcher.txt @@ -1748,7 +1829,10 @@ share/doc/EMBOSS/programs/text/needle.txt share/doc/EMBOSS/programs/text/newcpgreport.txt share/doc/EMBOSS/programs/text/newcpgseek.txt share/doc/EMBOSS/programs/text/newseq.txt +share/doc/EMBOSS/programs/text/nohtml.txt share/doc/EMBOSS/programs/text/noreturn.txt +share/doc/EMBOSS/programs/text/nospace.txt +share/doc/EMBOSS/programs/text/notab.txt share/doc/EMBOSS/programs/text/notseq.txt share/doc/EMBOSS/programs/text/nthseq.txt share/doc/EMBOSS/programs/text/octanol.txt @@ -1799,6 +1883,8 @@ share/doc/EMBOSS/programs/text/sigcleave.txt share/doc/EMBOSS/programs/text/silent.txt share/doc/EMBOSS/programs/text/sirna.txt share/doc/EMBOSS/programs/text/sixpack.txt +share/doc/EMBOSS/programs/text/sizeseq.txt +share/doc/EMBOSS/programs/text/skipredundant.txt share/doc/EMBOSS/programs/text/skipseq.txt share/doc/EMBOSS/programs/text/splitter.txt share/doc/EMBOSS/programs/text/stretcher.txt @@ -1815,6 +1901,7 @@ share/doc/EMBOSS/programs/text/tranalign.txt share/doc/EMBOSS/programs/text/transeq.txt share/doc/EMBOSS/programs/text/trimest.txt share/doc/EMBOSS/programs/text/trimseq.txt +share/doc/EMBOSS/programs/text/trimspace.txt share/doc/EMBOSS/programs/text/twofeat.txt share/doc/EMBOSS/programs/text/union.txt share/doc/EMBOSS/programs/text/vectorstrip.txt