1 files changed, 370 insertions, 361 deletions

diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 17f29251c4bd..fed75c0b709d 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -10,6 +10,7 @@ bin/cirdna
 bin/codcmp
 bin/complex
 bin/compseq
+bin/cons
 bin/cpgplot
 bin/cpgreport
 bin/cusp
@@ -26,7 +27,6 @@ bin/dotmatcher
 bin/dotpath
 bin/dottup
 bin/dreg
-bin/iep
 bin/einverted
 bin/embossdata
 bin/emma
@@ -44,6 +44,7 @@ bin/garnier
 bin/geecee
 bin/getorf
 bin/helixturnhelix
+bin/iep
 bin/infoseq
 bin/isochore
 bin/lindna
@@ -72,6 +73,7 @@ bin/pepstats
 bin/pepwheel
 bin/pepwindow
 bin/pepwindowall
+bin/plotcon
 bin/plotorf
 bin/polydot
 bin/preg
@@ -109,8 +111,8 @@ bin/stssearch
 bin/supermatcher
 bin/syco
 bin/textsearch
-bin/tfm
 bin/tfextract
+bin/tfm
 bin/tfscan
 bin/tmap
 bin/transeq
@@ -122,337 +124,18 @@ bin/wordcount
 bin/wordmatch
 bin/wossname
 etc/emboss.default.sample
-lib/libplplot.so.4
-lib/libplplot.so
-lib/libplplot.a
-lib/libajax.so.1
-lib/libajax.so
 lib/libajax.a
-lib/libajaxg.so.1
-lib/libajaxg.so
+lib/libajax.so
+lib/libajax.so.1
 lib/libajaxg.a
-lib/libnucleus.so.1
-lib/libnucleus.so
+lib/libajaxg.so
+lib/libajaxg.so.1
 lib/libnucleus.a
-share/doc/EMBOSS/manuals/admin.sty
-share/doc/EMBOSS/manuals/admin.tex
-share/doc/EMBOSS/programs/html/SITE-DIRECTED.html
-share/doc/EMBOSS/programs/html/alignment_global_group.html
-share/doc/EMBOSS/programs/html/alignment_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/chaos.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/codcmp.html
-share/doc/EMBOSS/programs/html/coding_regions_group.html
-share/doc/EMBOSS/programs/html/comparison_group.html
-share/doc/EMBOSS/programs/html/complex.html
-share/doc/EMBOSS/programs/html/compseq.html
-share/doc/EMBOSS/programs/html/cpgplot.html
-share/doc/EMBOSS/programs/html/cpg_islands_group.html
-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/database_entry_extraction_group.html
-share/doc/EMBOSS/programs/html/database_indexing_group.html
-share/doc/EMBOSS/programs/html/database_information_group.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/descseq.html
-share/doc/EMBOSS/programs/html/diffseq.html
-share/doc/EMBOSS/programs/html/digest.html
-share/doc/EMBOSS/programs/html/display_alignment_multiple_group.html
-share/doc/EMBOSS/programs/html/dna_sequence_composition_group.html
-share/doc/EMBOSS/programs/html/dna_sequence_features_group.html
-share/doc/EMBOSS/programs/html/dna_sequence_properties_group.html
-share/doc/EMBOSS/programs/html/dotmatcher.html
-share/doc/EMBOSS/programs/html/dotpath.html
-share/doc/EMBOSS/programs/html/dottup.html
-share/doc/EMBOSS/programs/html/dreg.html
-share/doc/EMBOSS/programs/html/einverted.html
-share/doc/EMBOSS/programs/html/embossdata.html
-share/doc/EMBOSS/programs/html/emma.html
-share/doc/EMBOSS/programs/html/enzyme_kinetics_group.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/extractseq.html
-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/geecee.html
-share/doc/EMBOSS/programs/html/garnier.html
-share/doc/EMBOSS/programs/html/gene_finding_group.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/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
-share/doc/EMBOSS/programs/html/lindna.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/merger.html
-share/doc/EMBOSS/programs/html/motifs_group.html
-share/doc/EMBOSS/programs/html/msbar.html
-share/doc/EMBOSS/programs/html/mutation_group.html
-share/doc/EMBOSS/programs/html/needle.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
-share/doc/EMBOSS/programs/html/noreturn.html
-share/doc/EMBOSS/programs/html/nthseq.html
-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/pattern_matching_group.html
-share/doc/EMBOSS/programs/html/pepcoil.html
-share/doc/EMBOSS/programs/html/pepinfo.html
-share/doc/EMBOSS/programs/html/pepnet.html
-share/doc/EMBOSS/programs/html/pepstats.html
-share/doc/EMBOSS/programs/html/pepwheel.html
-share/doc/EMBOSS/programs/html/pepwindow.html
-share/doc/EMBOSS/programs/html/pepwindowall.html
-share/doc/EMBOSS/programs/html/plotorf.html
-share/doc/EMBOSS/programs/html/preg.html
-share/doc/EMBOSS/programs/html/polydot.html
-share/doc/EMBOSS/programs/html/prettyplot.html
-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
-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/pscan.html
-share/doc/EMBOSS/programs/html/rebaseextract.html
-share/doc/EMBOSS/programs/html/redata.html
-share/doc/EMBOSS/programs/html/reformatting_group.html
-share/doc/EMBOSS/programs/html/remap.html
-share/doc/EMBOSS/programs/html/repeats_group.html
-share/doc/EMBOSS/programs/html/restrict.html
-share/doc/EMBOSS/programs/html/restriction_enzymes_group.html
-share/doc/EMBOSS/programs/html/revseq.html
-share/doc/EMBOSS/programs/html/secondary_structure_group.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/seqretall.html
-share/doc/EMBOSS/programs/html/seqretset.html
-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/showdb.html
-share/doc/EMBOSS/programs/html/sequence_information_group.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/site_directed_mutagenesis_group.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.html
-share/doc/EMBOSS/programs/html/text_search_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.html
-share/doc/EMBOSS/programs/html/transeq.html
-share/doc/EMBOSS/programs/html/transcription_group.html
-share/doc/EMBOSS/programs/html/translation_group.html
-share/doc/EMBOSS/programs/html/trimseq.html
-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/vectorstrip.html
-share/doc/EMBOSS/programs/html/water.html
-share/doc/EMBOSS/programs/html/wobble.html
-share/doc/EMBOSS/programs/html/wordcount.html
-share/doc/EMBOSS/programs/html/wordmatch.html
-share/doc/EMBOSS/programs/html/wossname.html
-share/doc/EMBOSS/programs/html/banana0.gif
-share/doc/EMBOSS/programs/html/chaos0.gif
-share/doc/EMBOSS/programs/html/cpgplot0.gif
-share/doc/EMBOSS/programs/html/dotmatcher0.gif
-share/doc/EMBOSS/programs/html/dottup0.gif
-share/doc/EMBOSS/programs/html/emboss_icon.gif
-share/doc/EMBOSS/programs/html/findkm0.gif
-share/doc/EMBOSS/programs/html/isochore0.gif
-share/doc/EMBOSS/programs/html/octanol0.gif
-share/doc/EMBOSS/programs/html/pepinfo1.gif
-share/doc/EMBOSS/programs/html/pepinfo2.gif
-share/doc/EMBOSS/programs/html/pepnet0.gif
-share/doc/EMBOSS/programs/html/pepwheel0.gif
-share/doc/EMBOSS/programs/html/pepwindow0.gif
-share/doc/EMBOSS/programs/html/pepwindowall0.gif
-share/doc/EMBOSS/programs/html/plotorf0.gif
-share/doc/EMBOSS/programs/html/polydot0.gif
-share/doc/EMBOSS/programs/html/prettyplot3.gif
-share/doc/EMBOSS/programs/html/prettyplot4.gif
-share/doc/EMBOSS/programs/html/syco0.gif
-share/doc/EMBOSS/programs/html/syco1.gif
-share/doc/EMBOSS/programs/html/tmap0.gif
-share/doc/EMBOSS/programs/html/wobble0.gif
-share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt
-share/doc/EMBOSS/programs/text/antigenic.txt
-share/doc/EMBOSS/programs/text/backtranseq.txt
-share/doc/EMBOSS/programs/text/banana.txt
-share/doc/EMBOSS/programs/text/btwisted.txt
-share/doc/EMBOSS/programs/text/chaos.txt
-share/doc/EMBOSS/programs/text/checktrans.txt
-share/doc/EMBOSS/programs/text/chips.txt
-share/doc/EMBOSS/programs/text/cirdna.txt
-share/doc/EMBOSS/programs/text/codcmp.txt
-share/doc/EMBOSS/programs/text/complex.txt
-share/doc/EMBOSS/programs/text/compseq.txt
-share/doc/EMBOSS/programs/text/cpgplot.txt
-share/doc/EMBOSS/programs/text/cpgreport.txt
-share/doc/EMBOSS/programs/text/cusp.txt
-share/doc/EMBOSS/programs/text/cutseq.txt
-share/doc/EMBOSS/programs/text/dan.txt
-share/doc/EMBOSS/programs/text/dbiblast.txt
-share/doc/EMBOSS/programs/text/dbifasta.txt
-share/doc/EMBOSS/programs/text/dbiflat.txt
-share/doc/EMBOSS/programs/text/dbigcg.txt
-share/doc/EMBOSS/programs/text/descseq.txt
-share/doc/EMBOSS/programs/text/iep.txt
-share/doc/EMBOSS/programs/text/diffseq.txt
-share/doc/EMBOSS/programs/text/digest.txt
-share/doc/EMBOSS/programs/text/dotmatcher.txt
-share/doc/EMBOSS/programs/text/dotpath.txt
-share/doc/EMBOSS/programs/text/dottup.txt
-share/doc/EMBOSS/programs/text/dreg.txt
-share/doc/EMBOSS/programs/text/einverted.txt
-share/doc/EMBOSS/programs/text/embossdata.txt
-share/doc/EMBOSS/programs/text/emma.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/extractseq.txt
-share/doc/EMBOSS/programs/text/findkm.txt
-share/doc/EMBOSS/programs/text/freak.txt
-share/doc/EMBOSS/programs/text/fuzznuc.txt
-share/doc/EMBOSS/programs/text/fuzzpro.txt
-share/doc/EMBOSS/programs/text/fuzztran.txt
-share/doc/EMBOSS/programs/text/garnier.txt
-share/doc/EMBOSS/programs/text/geecee.txt
-share/doc/EMBOSS/programs/text/getorf.txt
-share/doc/EMBOSS/programs/text/helixturnhelix.txt
-share/doc/EMBOSS/programs/text/infoseq.txt
-share/doc/EMBOSS/programs/text/isochore.txt
-share/doc/EMBOSS/programs/text/lindna.txt
-share/doc/EMBOSS/programs/text/maskfeat.txt
-share/doc/EMBOSS/programs/text/maskseq.txt
-share/doc/EMBOSS/programs/text/matcher.txt
-share/doc/EMBOSS/programs/text/megamerger.txt
-share/doc/EMBOSS/programs/text/merger.txt
-share/doc/EMBOSS/programs/text/msbar.txt
-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/noreturn.txt
-share/doc/EMBOSS/programs/text/nthseq.txt
-share/doc/EMBOSS/programs/text/octanol.txt
-share/doc/EMBOSS/programs/text/oddcomp.txt
-share/doc/EMBOSS/programs/text/palindrome.txt
-share/doc/EMBOSS/programs/text/pasteseq.txt
-share/doc/EMBOSS/programs/text/patmatdb.txt
-share/doc/EMBOSS/programs/text/patmatmotifs.txt
-share/doc/EMBOSS/programs/text/pepcoil.txt
-share/doc/EMBOSS/programs/text/pepinfo.txt
-share/doc/EMBOSS/programs/text/pepnet.txt
-share/doc/EMBOSS/programs/text/pepstats.txt
-share/doc/EMBOSS/programs/text/pepwheel.txt
-share/doc/EMBOSS/programs/text/pepwindow.txt
-share/doc/EMBOSS/programs/text/pepwindowall.txt
-share/doc/EMBOSS/programs/text/plotorf.txt
-share/doc/EMBOSS/programs/text/polydot.txt
-share/doc/EMBOSS/programs/text/preg.txt
-share/doc/EMBOSS/programs/text/prettyplot.txt
-share/doc/EMBOSS/programs/text/prettyseq.txt
-share/doc/EMBOSS/programs/text/prima.txt
-share/doc/EMBOSS/programs/text/primersearch.txt
-share/doc/EMBOSS/programs/text/printsextract.txt
-share/doc/EMBOSS/programs/text/profit.txt
-share/doc/EMBOSS/programs/text/prophecy.txt
-share/doc/EMBOSS/programs/text/prophet.txt
-share/doc/EMBOSS/programs/text/prosextract.txt
-share/doc/EMBOSS/programs/text/pscan.txt
-share/doc/EMBOSS/programs/text/rebaseextract.txt
-share/doc/EMBOSS/programs/text/redata.txt
-share/doc/EMBOSS/programs/text/remap.txt
-share/doc/EMBOSS/programs/text/restrict.txt
-share/doc/EMBOSS/programs/text/revseq.txt
-share/doc/EMBOSS/programs/text/seealso.txt
-share/doc/EMBOSS/programs/text/seqmatchall.txt
-share/doc/EMBOSS/programs/text/seqret.txt
-share/doc/EMBOSS/programs/text/seqretall.txt
-share/doc/EMBOSS/programs/text/seqretset.txt
-share/doc/EMBOSS/programs/text/showdb.txt
-share/doc/EMBOSS/programs/text/showfeat.txt
-share/doc/EMBOSS/programs/text/showorf.txt
-share/doc/EMBOSS/programs/text/showseq.txt
-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/stretcher.txt
-share/doc/EMBOSS/programs/text/stssearch.txt
-share/doc/EMBOSS/programs/text/supermatcher.txt
-share/doc/EMBOSS/programs/text/syco.txt
-share/doc/EMBOSS/programs/text/textsearch.txt
-share/doc/EMBOSS/programs/text/tfextract.txt
-share/doc/EMBOSS/programs/text/tfm.txt
-share/doc/EMBOSS/programs/text/tfscan.txt
-share/doc/EMBOSS/programs/text/tmap.txt
-share/doc/EMBOSS/programs/text/transeq.txt
-share/doc/EMBOSS/programs/text/trimseq.txt
-share/doc/EMBOSS/programs/text/vectorstrip.txt
-share/doc/EMBOSS/programs/text/water.txt
-share/doc/EMBOSS/programs/text/wobble.txt
-share/doc/EMBOSS/programs/text/wordcount.txt
-share/doc/EMBOSS/programs/text/wordmatch.txt
-share/doc/EMBOSS/programs/text/wossname.txt
-share/doc/EMBOSS/tutorials/biblio.bib
-share/doc/EMBOSS/tutorials/emboss_tutorial.tex
-share/doc/EMBOSS/tutorials/dottup.ps
-share/doc/EMBOSS/tutorials/pepinfo1.ps
-share/doc/EMBOSS/tutorials/pepinfo2.ps
-share/doc/EMBOSS/tutorials/plotorf.ps
-share/doc/EMBOSS/tutorials/tmap.ps
-share/EMBOSS/plstnd5.fnt
-share/EMBOSS/plxtnd5.fnt
+lib/libnucleus.so
+lib/libnucleus.so.1
+lib/libplplot.a
+lib/libplplot.so
+lib/libplplot.so.4
 share/EMBOSS/acd/ajbad.acd
 share/EMBOSS/acd/ajfeatest.acd
 share/EMBOSS/acd/ajtest.acd
@@ -467,8 +150,10 @@ share/EMBOSS/acd/chips.acd
 share/EMBOSS/acd/cirdna.acd
 share/EMBOSS/acd/cluster.acd
 share/EMBOSS/acd/codcmp.acd
+share/EMBOSS/acd/codes.english
 share/EMBOSS/acd/complex.acd
 share/EMBOSS/acd/compseq.acd
+share/EMBOSS/acd/cons.acd
 share/EMBOSS/acd/cpgplot.acd
 share/EMBOSS/acd/cpgreport.acd
 share/EMBOSS/acd/cusp.acd
@@ -491,6 +176,7 @@ 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/emma.acd
 share/EMBOSS/acd/emowse.acd
@@ -498,7 +184,6 @@ share/EMBOSS/acd/entrails.acd
 share/EMBOSS/acd/equicktandem.acd
 share/EMBOSS/acd/est2genome.acd
 share/EMBOSS/acd/etandem.acd
-share/EMBOSS/acd/iep.acd
 share/EMBOSS/acd/extractseq.acd
 share/EMBOSS/acd/findkm.acd
 share/EMBOSS/acd/freak.acd
@@ -510,6 +195,7 @@ share/EMBOSS/acd/geecee.acd
 share/EMBOSS/acd/getorf.acd
 share/EMBOSS/acd/helixturnhelix.acd
 share/EMBOSS/acd/histogramtest.acd
+share/EMBOSS/acd/iep.acd
 share/EMBOSS/acd/infoseq.acd
 share/EMBOSS/acd/isochore.acd
 share/EMBOSS/acd/lindna.acd
@@ -539,12 +225,12 @@ share/EMBOSS/acd/pepstats.acd
 share/EMBOSS/acd/pepwheel.acd
 share/EMBOSS/acd/pepwindow.acd
 share/EMBOSS/acd/pepwindowall.acd
+share/EMBOSS/acd/plotcon.acd
 share/EMBOSS/acd/plotorf.acd
 share/EMBOSS/acd/plplottest.acd
 share/EMBOSS/acd/polydot.acd
 share/EMBOSS/acd/preg.acd
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+share/doc/EMBOSS/programs/text/remap.txt
+share/doc/EMBOSS/programs/text/restrict.txt
+share/doc/EMBOSS/programs/text/revseq.txt
+share/doc/EMBOSS/programs/text/seealso.txt
+share/doc/EMBOSS/programs/text/seqmatchall.txt
+share/doc/EMBOSS/programs/text/seqret.txt
+share/doc/EMBOSS/programs/text/seqretall.txt
+share/doc/EMBOSS/programs/text/seqretset.txt
+share/doc/EMBOSS/programs/text/showdb.txt
+share/doc/EMBOSS/programs/text/showfeat.txt
+share/doc/EMBOSS/programs/text/showorf.txt
+share/doc/EMBOSS/programs/text/showseq.txt
+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/stretcher.txt
+share/doc/EMBOSS/programs/text/stssearch.txt
+share/doc/EMBOSS/programs/text/supermatcher.txt
+share/doc/EMBOSS/programs/text/syco.txt
+share/doc/EMBOSS/programs/text/textsearch.txt
+share/doc/EMBOSS/programs/text/tfextract.txt
+share/doc/EMBOSS/programs/text/tfm.txt
+share/doc/EMBOSS/programs/text/tfscan.txt
+share/doc/EMBOSS/programs/text/tmap.txt
+share/doc/EMBOSS/programs/text/transeq.txt
+share/doc/EMBOSS/programs/text/trimseq.txt
+share/doc/EMBOSS/programs/text/vectorstrip.txt
+share/doc/EMBOSS/programs/text/water.txt
+share/doc/EMBOSS/programs/text/wobble.txt
+share/doc/EMBOSS/programs/text/wordcount.txt
+share/doc/EMBOSS/programs/text/wordmatch.txt
+share/doc/EMBOSS/programs/text/wossname.txt
+share/doc/EMBOSS/tutorials/biblio.bib
+share/doc/EMBOSS/tutorials/dottup.ps.gz
+share/doc/EMBOSS/tutorials/emboss_tutorial.tex
+share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
+share/doc/EMBOSS/tutorials/pepinfo2.ps.gz
+share/doc/EMBOSS/tutorials/plotorf.ps.gz
+share/doc/EMBOSS/tutorials/tmap.ps.gz
+@dirrm share/doc/EMBOSS/tutorials
 @dirrm share/doc/EMBOSS/programs/text
+@dirrm share/doc/EMBOSS/programs/html
 @dirrm share/doc/EMBOSS/programs
-@dirrm share/doc/EMBOSS/tutorials
+@dirrm share/doc/EMBOSS/manuals
 @dirrm share/doc/EMBOSS
-@dirrm share/EMBOSS/acd
-@dirrm share/EMBOSS/data/CODONS
+@dirrm share/EMBOSS/test/wormpep
+@dirrm share/EMBOSS/test/swnew
+@dirrm share/EMBOSS/test/swiss
+@dirrm share/EMBOSS/test/pir
+@dirrm share/EMBOSS/test/embl
+@dirrm share/EMBOSS/test/data
+@dirrm share/EMBOSS/test
 @dirrm share/EMBOSS/data/REBASE
-@dirrm share/EMBOSS/data/PRINTS
 @dirrm share/EMBOSS/data/PROSITE
+@dirrm share/EMBOSS/data/PRINTS
+@dirrm share/EMBOSS/data/CODONS
 @dirrm share/EMBOSS/data
-@dirrm share/EMBOSS/test/data
-@dirrm share/EMBOSS/test/embl
-@dirrm share/EMBOSS/test/pir
-@dirrm share/EMBOSS/test/swiss
-@dirrm share/EMBOSS/test/swnew
-@dirrm share/EMBOSS/test/wormpep
-@dirrm share/EMBOSS/test
+@dirrm share/EMBOSS/acd
 @dirrm share/EMBOSS