1 files changed, 172 insertions, 32 deletions

diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 172d5aa71752..8ce5313cae3f 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -93,6 +93,7 @@ bin/dottup
 bin/dreg
 bin/einverted
 bin/embossdata
+bin/embossversion
 bin/emma
 bin/emowse
 bin/entret
@@ -157,7 +158,7 @@ bin/prophet
 bin/prosextract
 bin/pscan
 bin/rebaseextract
-bin/recode
+bin/recoder
 bin/redata
 bin/remap
 bin/restover
@@ -171,6 +172,7 @@ bin/seqret
 bin/seqretall
 bin/seqretset
 bin/seqretsplit
+bin/showalign
 bin/showdb
 bin/showfeat
 bin/showorf
@@ -255,8 +257,8 @@ share/EMBOSS/acd/dotpath.acd
 share/EMBOSS/acd/dottup.acd
 share/EMBOSS/acd/dreg.acd
 share/EMBOSS/acd/einverted.acd
-share/EMBOSS/acd/emboss.default
 share/EMBOSS/acd/embossdata.acd
+share/EMBOSS/acd/embossversion.acd
 share/EMBOSS/acd/emma.acd
 share/EMBOSS/acd/emowse.acd
 share/EMBOSS/acd/entrails.acd
@@ -326,7 +328,7 @@ share/EMBOSS/acd/prosextract.acd
 share/EMBOSS/acd/proteinmotifsearch.acd
 share/EMBOSS/acd/pscan.acd
 share/EMBOSS/acd/rebaseextract.acd
-share/EMBOSS/acd/recode.acd
+share/EMBOSS/acd/recoder.acd
 share/EMBOSS/acd/redata.acd
 share/EMBOSS/acd/remap.acd
 share/EMBOSS/acd/restover.acd
@@ -344,6 +346,7 @@ share/EMBOSS/acd/seqretset.acd
 share/EMBOSS/acd/seqretsplit.acd
 share/EMBOSS/acd/seqrettype.acd
 share/EMBOSS/acd/seqtofeat.acd
+share/EMBOSS/acd/showalign.acd
 share/EMBOSS/acd/showdb.acd
 share/EMBOSS/acd/showfeat.acd
 share/EMBOSS/acd/showorf.acd
@@ -646,6 +649,7 @@ share/EMBOSS/data/PRINTS/dummyfile
 share/EMBOSS/data/PROSITE/dummyfile
 share/EMBOSS/data/REBASE/dummyfile
 share/EMBOSS/data/embossre.equ
+share/EMBOSS/emboss.default.template
 share/EMBOSS/plstnd5.fnt
 share/EMBOSS/plxtnd5.fnt
 share/EMBOSS/test/data/dna.acedb
@@ -674,6 +678,7 @@ share/EMBOSS/test/data/dna.phylip3
 share/EMBOSS/test/data/dna.staden
 share/EMBOSS/test/data/dna.strider
 share/EMBOSS/test/data/dna.text
+share/EMBOSS/test/data/paamir.pep
 share/EMBOSS/test/data/prot.acedb
 share/EMBOSS/test/data/prot.codata
 share/EMBOSS/test/data/prot.fasta
@@ -695,6 +700,7 @@ share/EMBOSS/test/embl/acnum.trg
 share/EMBOSS/test/embl/division.lkp
 share/EMBOSS/test/embl/entrynam.idx
 share/EMBOSS/test/embl/est.dat
+share/EMBOSS/test/embl/fun.dat
 share/EMBOSS/test/embl/hum1.dat
 share/EMBOSS/test/embl/inv.dat
 share/EMBOSS/test/embl/pro.dat
@@ -755,14 +761,127 @@ share/doc/EMBOSS/manuals/adminguide.tar.gz
 share/doc/EMBOSS/manuals/emboss_qg.pdf
 share/doc/EMBOSS/manuals/emboss_qg.ps
 share/doc/EMBOSS/manuals/program.ps.gz
+share/doc/EMBOSS/programs/html/abiview.html
 share/doc/EMBOSS/programs/html/abiview0.gif
+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/backtranseq.html
+share/doc/EMBOSS/programs/html/banana.html
 share/doc/EMBOSS/programs/html/banana0.gif
+share/doc/EMBOSS/programs/html/btwisted.html
+share/doc/EMBOSS/programs/html/cai.html
+share/doc/EMBOSS/programs/html/chaos.html
 share/doc/EMBOSS/programs/html/chaos0.gif
+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.html
+share/doc/EMBOSS/programs/html/clique.html
+share/doc/EMBOSS/programs/html/codcmp.html
+share/doc/EMBOSS/programs/html/coderet.html
+share/doc/EMBOSS/programs/html/compseq.html
+share/doc/EMBOSS/programs/html/cons.html
+share/doc/EMBOSS/programs/html/consense.html
+share/doc/EMBOSS/programs/html/contml.html
+share/doc/EMBOSS/programs/html/contrast.html
+share/doc/EMBOSS/programs/html/cpgplot.html
 share/doc/EMBOSS/programs/html/cpgplot0.gif
+share/doc/EMBOSS/programs/html/cpgreport.html
+share/doc/EMBOSS/programs/html/cusp.html
+share/doc/EMBOSS/programs/html/cutseq.html
+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/degapseq.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/dnacomp.html
+share/doc/EMBOSS/programs/html/dnadist.html
+share/doc/EMBOSS/programs/html/dnainvar.html
+share/doc/EMBOSS/programs/html/dnaml.html
+share/doc/EMBOSS/programs/html/dnamlk.html
+share/doc/EMBOSS/programs/html/dnapars.html
+share/doc/EMBOSS/programs/html/dnapenny.html
+share/doc/EMBOSS/programs/html/dollop.html
+share/doc/EMBOSS/programs/html/dolpenny.html
+share/doc/EMBOSS/programs/html/domainer.html
+share/doc/EMBOSS/programs/html/dotmatcher.html
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+share/doc/EMBOSS/programs/html/dotpath.html
+share/doc/EMBOSS/programs/html/dottup.html
 share/doc/EMBOSS/programs/html/dottup0.gif
+share/doc/EMBOSS/programs/html/dreg.html
+share/doc/EMBOSS/programs/html/eclique.html
+share/doc/EMBOSS/programs/html/econsense.html
+share/doc/EMBOSS/programs/html/econtml.html
+share/doc/EMBOSS/programs/html/econtrast.html
+share/doc/EMBOSS/programs/html/edit_group.html
+share/doc/EMBOSS/programs/html/ednacomp.html
+share/doc/EMBOSS/programs/html/ednadist.html
+share/doc/EMBOSS/programs/html/ednainvar.html
+share/doc/EMBOSS/programs/html/ednaml.html
+share/doc/EMBOSS/programs/html/ednamlk.html
+share/doc/EMBOSS/programs/html/ednapars.html
+share/doc/EMBOSS/programs/html/ednapenny.html
+share/doc/EMBOSS/programs/html/edollop.html
+share/doc/EMBOSS/programs/html/edolpenny.html
+share/doc/EMBOSS/programs/html/efactor.html
+share/doc/EMBOSS/programs/html/efitch.html
+share/doc/EMBOSS/programs/html/egendist.html
+share/doc/EMBOSS/programs/html/einverted.html
+share/doc/EMBOSS/programs/html/ekitsch.html
 share/doc/EMBOSS/programs/html/emboss_icon.gif
+share/doc/EMBOSS/programs/html/embossdata.html
+share/doc/EMBOSS/programs/html/embossversion.html
+share/doc/EMBOSS/programs/html/emix.html
+share/doc/EMBOSS/programs/html/emma.html
+share/doc/EMBOSS/programs/html/emowse.html
+share/doc/EMBOSS/programs/html/eneighbor.html
+share/doc/EMBOSS/programs/html/entret.html
+share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
+share/doc/EMBOSS/programs/html/epenny.html
+share/doc/EMBOSS/programs/html/eprotdist.html
+share/doc/EMBOSS/programs/html/eprotpars.html
+share/doc/EMBOSS/programs/html/equicktandem.html
+share/doc/EMBOSS/programs/html/erestml.html
+share/doc/EMBOSS/programs/html/eseqboot.html
+share/doc/EMBOSS/programs/html/est2genome.html
+share/doc/EMBOSS/programs/html/etandem.html
+share/doc/EMBOSS/programs/html/extractseq.html
+share/doc/EMBOSS/programs/html/factor.html
+share/doc/EMBOSS/programs/html/feature_tables_group.html
+share/doc/EMBOSS/programs/html/findkm.html
 share/doc/EMBOSS/programs/html/findkm0.gif
+share/doc/EMBOSS/programs/html/fitch.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/gendist.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/hmoment.html
+share/doc/EMBOSS/programs/html/iep.html
+share/doc/EMBOSS/programs/html/index.html
+share/doc/EMBOSS/programs/html/information_group.html
+share/doc/EMBOSS/programs/html/infoseq.html
+share/doc/EMBOSS/programs/html/isochore.html
+share/doc/EMBOSS/programs/html/isochore0.gif
+share/doc/EMBOSS/programs/html/kitsch.html
+share/doc/EMBOSS/programs/html/lindna.gif
 share/doc/EMBOSS/programs/html/lindna.html
 share/doc/EMBOSS/programs/html/marscan.html
 share/doc/EMBOSS/programs/html/maskfeat.html
@@ -772,13 +891,10 @@ 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/mix.html
-share/doc/EMBOSS/programs/html/motifs_group.html
 share/doc/EMBOSS/programs/html/msbar.html
 share/doc/EMBOSS/programs/html/mse.html
-share/doc/EMBOSS/programs/html/mutation_group.html
 share/doc/EMBOSS/programs/html/needle.html
 share/doc/EMBOSS/programs/html/neighbor.html
-share/doc/EMBOSS/programs/html/new_group_group.html
 share/doc/EMBOSS/programs/html/newcpgreport.html
 share/doc/EMBOSS/programs/html/newcpgseek.html
 share/doc/EMBOSS/programs/html/newseq.html
@@ -786,70 +902,86 @@ share/doc/EMBOSS/programs/html/noreturn.html
 share/doc/EMBOSS/programs/html/notseq.html
 share/doc/EMBOSS/programs/html/nrscope.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_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_transcription_group.html
+share/doc/EMBOSS/programs/html/nucleic_translation_group.html
 share/doc/EMBOSS/programs/html/octanol.html
+share/doc/EMBOSS/programs/html/octanol0.gif
 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/pattern_matching_group.html
 share/doc/EMBOSS/programs/html/penny.html
 share/doc/EMBOSS/programs/html/pepcoil.html
 share/doc/EMBOSS/programs/html/pepinfo.html
+share/doc/EMBOSS/programs/html/pepinfo1.gif
+share/doc/EMBOSS/programs/html/pepinfo2.gif
 share/doc/EMBOSS/programs/html/pepnet.html
+share/doc/EMBOSS/programs/html/pepnet0.gif
 share/doc/EMBOSS/programs/html/pepstats.html
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+share/doc/EMBOSS/programs/html/pepwheel0.gif
 share/doc/EMBOSS/programs/html/pepwindow.html
+share/doc/EMBOSS/programs/html/pepwindow0.gif
 share/doc/EMBOSS/programs/html/pepwindowall.html
+share/doc/EMBOSS/programs/html/pepwindowall0.gif
 share/doc/EMBOSS/programs/html/phylogeny_group.html
 share/doc/EMBOSS/programs/html/plotcon.html
 share/doc/EMBOSS/programs/html/plotorf.html
+share/doc/EMBOSS/programs/html/plotorf0.gif
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+share/doc/EMBOSS/programs/html/polydot0.gif
 share/doc/EMBOSS/programs/html/preg.html
 share/doc/EMBOSS/programs/html/prettyplot.html
+share/doc/EMBOSS/programs/html/prettyplot3.gif
+share/doc/EMBOSS/programs/html/prettyplot4.gif
 share/doc/EMBOSS/programs/html/prettyseq.html
 share/doc/EMBOSS/programs/html/prima.html
-share/doc/EMBOSS/programs/html/primers_group.html
 share/doc/EMBOSS/programs/html/primersearch.html
 share/doc/EMBOSS/programs/html/printsextract.html
-share/doc/EMBOSS/programs/html/profiles_group.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
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-share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html
-share/doc/EMBOSS/programs/html/protein_sequence_features_group.html
-share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html
-share/doc/EMBOSS/programs/html/protein_structure_group.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/pscan.html
-share/doc/EMBOSS/programs/html/re_group.html
 share/doc/EMBOSS/programs/html/rebaseextract.html
 share/doc/EMBOSS/programs/html/recode.html
+share/doc/EMBOSS/programs/html/recoder.html
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-share/doc/EMBOSS/programs/html/reformatting_group.html
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-share/doc/EMBOSS/programs/html/repeats_group.html
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-share/doc/EMBOSS/programs/html/restriction_enzymes_group.html
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+share/doc/EMBOSS/programs/html/scopalign.html
 share/doc/EMBOSS/programs/html/scope.html
-share/doc/EMBOSS/programs/html/secondary_structure_group.html
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 share/doc/EMBOSS/programs/html/seqmatchall.html
 share/doc/EMBOSS/programs/html/seqret.html
 share/doc/EMBOSS/programs/html/seqretall.html
+share/doc/EMBOSS/programs/html/seqretfeat.html
 share/doc/EMBOSS/programs/html/seqretset.html
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-share/doc/EMBOSS/programs/html/sequence_comparison_group.html
-share/doc/EMBOSS/programs/html/sequence_composition_group.html
-share/doc/EMBOSS/programs/html/sequence_display_group.html
-share/doc/EMBOSS/programs/html/sequence_editing_group.html
-share/doc/EMBOSS/programs/html/sequence_features_group.html
-share/doc/EMBOSS/programs/html/sequence_information_group.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
@@ -857,29 +989,32 @@ 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/site_directed_mutagenesis_group.html
 share/doc/EMBOSS/programs/html/splitter.html
+share/doc/EMBOSS/programs/html/stamps.html
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-share/doc/EMBOSS/programs/html/text_search_group.html
+share/doc/EMBOSS/programs/html/syco0.gif
+share/doc/EMBOSS/programs/html/syco1.gif
+share/doc/EMBOSS/programs/html/test_group.html
 share/doc/EMBOSS/programs/html/textsearch.html
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 share/doc/EMBOSS/programs/html/tfm.html
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+share/doc/EMBOSS/programs/html/tmap0.gif
+share/doc/EMBOSS/programs/html/topo.gif
 share/doc/EMBOSS/programs/html/topo.html
-share/doc/EMBOSS/programs/html/transcription_group.html
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-share/doc/EMBOSS/programs/html/translation_group.html
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-share/doc/EMBOSS/programs/html/utilities_group.html
-share/doc/EMBOSS/programs/html/utilities_help_group.html
-share/doc/EMBOSS/programs/html/utilities_keyword_search_group.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
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+share/doc/EMBOSS/programs/html/wobble0.gif
 share/doc/EMBOSS/programs/html/wordcount.html
 share/doc/EMBOSS/programs/html/wordmatch.html
 share/doc/EMBOSS/programs/html/wossname.html
@@ -951,9 +1086,9 @@ share/doc/EMBOSS/programs/text/egendist.txt
 share/doc/EMBOSS/programs/text/einverted.txt
 share/doc/EMBOSS/programs/text/ekitsch.txt
 share/doc/EMBOSS/programs/text/embossdata.txt
+share/doc/EMBOSS/programs/text/embossversion.txt
 share/doc/EMBOSS/programs/text/emix.txt
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-share/doc/EMBOSS/programs/text/emnu.txt
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 share/doc/EMBOSS/programs/text/entret.txt
@@ -1033,20 +1168,24 @@ share/doc/EMBOSS/programs/text/protdist.txt
 share/doc/EMBOSS/programs/text/pscan.txt
 share/doc/EMBOSS/programs/text/rebaseextract.txt
 share/doc/EMBOSS/programs/text/recode.txt
+share/doc/EMBOSS/programs/text/recoder.txt
 share/doc/EMBOSS/programs/text/redata.txt
 share/doc/EMBOSS/programs/text/remap.txt
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 share/doc/EMBOSS/programs/text/restover.txt
 share/doc/EMBOSS/programs/text/restrict.txt
 share/doc/EMBOSS/programs/text/revseq.txt
+share/doc/EMBOSS/programs/text/scopalign.txt
 share/doc/EMBOSS/programs/text/scope.txt
 share/doc/EMBOSS/programs/text/seealso.txt
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 share/doc/EMBOSS/programs/text/seqmatchall.txt
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+share/doc/EMBOSS/programs/text/seqretfeat.txt
 share/doc/EMBOSS/programs/text/seqretset.txt
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+share/doc/EMBOSS/programs/text/showalign.txt
 share/doc/EMBOSS/programs/text/showdb.txt
 share/doc/EMBOSS/programs/text/showfeat.txt
 share/doc/EMBOSS/programs/text/showorf.txt
@@ -1055,6 +1194,7 @@ share/doc/EMBOSS/programs/text/shuffleseq.txt
 share/doc/EMBOSS/programs/text/sigcleave.txt
 share/doc/EMBOSS/programs/text/silent.txt
 share/doc/EMBOSS/programs/text/splitter.txt
+share/doc/EMBOSS/programs/text/stamps.txt
 share/doc/EMBOSS/programs/text/stretcher.txt
 share/doc/EMBOSS/programs/text/stssearch.txt
 share/doc/EMBOSS/programs/text/supermatcher.txt