5 files changed, 240 insertions, 42 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index e5a72d56e34f..eb18b8723f2a 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	1.12.0
+PORTVERSION=	1.13.1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
@@ -42,6 +42,7 @@ MSE_VERSION=	0.0.4
 TOPO_VERSION=	0.1
 PHYLIP_VERSION=	3.573c
 DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
+CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
 
 .for app in EMNU MSE PHYLIP TOPO
 SCRIPTS_ENV+=	${app}_VERSION="${${app}_VERSION}"
@@ -104,8 +105,7 @@ post-install:
 	  ${MAKE_ARGS} ${INSTALL_TARGET})
 .endfor
 	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
-	  ${WRKSRC}/emboss/acd/emboss.default > \
-	  ${PREFIX}/etc/emboss.default.sample && \
+	  ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
 	  ${CHOWN} ${SHAREOWN}:${SHAREGRP} \
 	  ${PREFIX}/etc/emboss.default.sample
 .if !defined(BATCH)
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index d30be07842a3..6d195e979827 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,5 +1,5 @@
-MD5 (emboss/EMBOSS-1.12.0.tar.gz) = 7d2d770dcc037624e5ee52c143c8923b
+MD5 (emboss/EMBOSS-1.13.1.tar.gz) = 313440f1c5f41cb8615f01dfba445358
 MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
-MD5 (emboss/MSE-0.0.4.tar.gz) = f490638c4f0b789d0c1117513406d76a
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4a4fff45f4a51a430731a46f3f37f37f
-MD5 (emboss/TOPO-0.1.tar.gz) = fa1a85bfde1054136af5aa9587c2433f
+MD5 (emboss/MSE-0.0.4.tar.gz) = 8b5e9cb6919be5cae1ea977ea7327e79
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = c001525bfbedc8903da34d859eeedf0c
+MD5 (emboss/TOPO-0.1.tar.gz) = c3ea9c55af1d48644f9096ac793cc5a1
diff --git a/biology/emboss/files/patch-emboss-acd-emboss.default b/biology/emboss/files/patch-emboss-emboss.default.template
index 1346c5d78ce6..3bbe6641a0d1 100644
--- a/biology/emboss/files/patch-emboss-acd-emboss.default
+++ b/biology/emboss/files/patch-emboss-emboss.default.template
@@ -1,7 +1,7 @@
---- emboss/acd/emboss.default.orig	Sun Feb 18 16:57:08 2001
-+++ emboss/acd/emboss.default	Tue Feb 20 10:45:57 2001
+--- emboss/emboss.default.template.orig	Thu May 24 19:36:39 2001
++++ emboss/emboss.default.template	Wed May 30 10:23:48 2001
 @@ -1,9 +1,31 @@
--SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
+-#SET emboss_tempdata name_of_emboss_test_database_directory
 +#####################################################
 +### Configuration options for FreeBSD EMBOSS port ###
 +#####################################################
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
 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/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
 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
 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/protdist.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/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
 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/restml.html
 share/doc/EMBOSS/programs/html/restover.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/scopalign.html
 share/doc/EMBOSS/programs/html/scope.html
-share/doc/EMBOSS/programs/html/secondary_structure_group.html
 share/doc/EMBOSS/programs/html/seealso.html
 share/doc/EMBOSS/programs/html/seqboot.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/seqretfeat.html
 share/doc/EMBOSS/programs/html/seqretset.html
 share/doc/EMBOSS/programs/html/seqretsplit.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/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
 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/syco0.gif
+share/doc/EMBOSS/programs/html/syco1.gif
+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.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
-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/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/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
@@ -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
 share/doc/EMBOSS/programs/text/emma.txt
-share/doc/EMBOSS/programs/text/emnu.txt
 share/doc/EMBOSS/programs/text/emowse.txt
 share/doc/EMBOSS/programs/text/eneighbor.txt
 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
 share/doc/EMBOSS/programs/text/restml.txt
 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
 share/doc/EMBOSS/programs/text/seqboot.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/seqretfeat.txt
 share/doc/EMBOSS/programs/text/seqretset.txt
 share/doc/EMBOSS/programs/text/seqretsplit.txt
+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
diff --git a/biology/emboss/pkg-plist.embassy b/biology/emboss/pkg-plist.embassy
new file mode 100644
index 000000000000..862a8acfecdc
--- /dev/null
+++ b/biology/emboss/pkg-plist.embassy
@@ -0,0 +1,58 @@
+%%PLIST_EMNU%%bin/emnu
+%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
+%%PLIST_MSE%%bin/mse
+%%PLIST_MSE%%lib/libckit.a
+%%PLIST_MSE%%lib/libckit.la
+%%PLIST_MSE%%lib/libckit.so
+%%PLIST_MSE%%lib/libckit.so.1
+%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
+%%PLIST_PHYLIP%%bin/eclique
+%%PLIST_PHYLIP%%bin/econsense
+%%PLIST_PHYLIP%%bin/econtml
+%%PLIST_PHYLIP%%bin/econtrast
+%%PLIST_PHYLIP%%bin/ednacomp
+%%PLIST_PHYLIP%%bin/ednadist
+%%PLIST_PHYLIP%%bin/ednainvar
+%%PLIST_PHYLIP%%bin/ednaml
+%%PLIST_PHYLIP%%bin/ednamlk
+%%PLIST_PHYLIP%%bin/ednapars
+%%PLIST_PHYLIP%%bin/ednapenny
+%%PLIST_PHYLIP%%bin/edollop
+%%PLIST_PHYLIP%%bin/edolpenny
+%%PLIST_PHYLIP%%bin/efactor
+%%PLIST_PHYLIP%%bin/efitch
+%%PLIST_PHYLIP%%bin/egendist
+%%PLIST_PHYLIP%%bin/ekitsch
+%%PLIST_PHYLIP%%bin/emix
+%%PLIST_PHYLIP%%bin/eneighbor
+%%PLIST_PHYLIP%%bin/epenny
+%%PLIST_PHYLIP%%bin/eprotdist
+%%PLIST_PHYLIP%%bin/eprotpars
+%%PLIST_PHYLIP%%bin/erestml
+%%PLIST_PHYLIP%%bin/eseqboot
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
+%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
+%%PLIST_TOPO%%bin/topo
+%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd