1 files changed, 20 insertions, 133 deletions

diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index b34528077b78..172d5aa71752 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -62,6 +62,7 @@ bin/antigenic
 bin/backtranseq
 bin/banana
 bin/btwisted
+bin/cai
 bin/chaos
 bin/charge
 bin/checktrans
@@ -84,6 +85,7 @@ bin/degapseq
 bin/descseq
 bin/diffseq
 bin/digest
+bin/distmat
 bin/domainer
 bin/dotmatcher
 bin/dotpath
@@ -161,6 +163,7 @@ bin/remap
 bin/restover
 bin/restrict
 bin/revseq
+bin/scopalign
 bin/scope
 bin/seealso
 bin/seqmatchall
@@ -215,6 +218,7 @@ share/EMBOSS/acd/antigenic.acd
 share/EMBOSS/acd/backtranseq.acd
 share/EMBOSS/acd/banana.acd
 share/EMBOSS/acd/btwisted.acd
+share/EMBOSS/acd/cai.acd
 share/EMBOSS/acd/chaos.acd
 share/EMBOSS/acd/charge.acd
 share/EMBOSS/acd/checktrans.acd
@@ -738,134 +742,27 @@ share/EMBOSS/test/wormpep/acnum.trg
 share/EMBOSS/test/wormpep/division.lkp
 share/EMBOSS/test/wormpep/entrynam.idx
 share/EMBOSS/test/wormpep/wormpep
+share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt
+share/doc/EMBOSS/manuals/admin.aux
+share/doc/EMBOSS/manuals/admin.dvi
+share/doc/EMBOSS/manuals/admin.log
+share/doc/EMBOSS/manuals/admin.pdf
+share/doc/EMBOSS/manuals/admin.ps
 share/doc/EMBOSS/manuals/admin.sty
 share/doc/EMBOSS/manuals/admin.tex
+share/doc/EMBOSS/manuals/admin.toc
+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/SITE-DIRECTED.html
-share/doc/EMBOSS/programs/html/abi_trace_files_group.html
-share/doc/EMBOSS/programs/html/abiview.html
 share/doc/EMBOSS/programs/html/abiview0.gif
-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/assorted_group.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/chaos.html
 share/doc/EMBOSS/programs/html/chaos0.gif
-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/coding_regions_group.html
-share/doc/EMBOSS/programs/html/comparison_group.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/cpg_islands_group.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/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/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_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/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
 share/doc/EMBOSS/programs/html/dotmatcher0.gif
-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/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/emix.html
-share/doc/EMBOSS/programs/html/emma.html
-share/doc/EMBOSS/programs/html/emnu.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/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/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/isochore0.gif
-share/doc/EMBOSS/programs/html/kitsch.html
 share/doc/EMBOSS/programs/html/lindna.html
 share/doc/EMBOSS/programs/html/marscan.html
 share/doc/EMBOSS/programs/html/maskfeat.html
@@ -890,7 +787,6 @@ 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/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
@@ -900,26 +796,17 @@ 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
 share/doc/EMBOSS/programs/html/pepwheel.html
-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
 share/doc/EMBOSS/programs/html/polydot.html
-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
@@ -976,16 +863,12 @@ 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/syco0.gif
-share/doc/EMBOSS/programs/html/syco1.gif
 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/tmap0.gif
-share/doc/EMBOSS/programs/html/topo.gif
 share/doc/EMBOSS/programs/html/topo.html
 share/doc/EMBOSS/programs/html/transcription_group.html
 share/doc/EMBOSS/programs/html/transeq.html
@@ -997,7 +880,6 @@ 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/wobble0.gif
 share/doc/EMBOSS/programs/html/wordcount.html
 share/doc/EMBOSS/programs/html/wordmatch.html
 share/doc/EMBOSS/programs/html/wossname.html
@@ -1007,7 +889,9 @@ 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/cai.txt
 share/doc/EMBOSS/programs/text/chaos.txt
+share/doc/EMBOSS/programs/text/charge.txt
 share/doc/EMBOSS/programs/text/checktrans.txt
 share/doc/EMBOSS/programs/text/chips.txt
 share/doc/EMBOSS/programs/text/cirdna.txt
@@ -1033,6 +917,7 @@ share/doc/EMBOSS/programs/text/degapseq.txt
 share/doc/EMBOSS/programs/text/descseq.txt
 share/doc/EMBOSS/programs/text/diffseq.txt
 share/doc/EMBOSS/programs/text/digest.txt
+share/doc/EMBOSS/programs/text/distmat.txt
 share/doc/EMBOSS/programs/text/dnacomp.txt
 share/doc/EMBOSS/programs/text/dnadist.txt
 share/doc/EMBOSS/programs/text/dnainvar.txt
@@ -1093,6 +978,7 @@ share/doc/EMBOSS/programs/text/geecee.txt
 share/doc/EMBOSS/programs/text/gendist.txt
 share/doc/EMBOSS/programs/text/getorf.txt
 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/infoseq.txt
 share/doc/EMBOSS/programs/text/isochore.txt
@@ -1189,6 +1075,7 @@ 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-talk.ppt
 share/doc/EMBOSS/tutorials/emboss_tutorial.tex
 share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
 share/doc/EMBOSS/tutorials/pepinfo2.ps.gz