- Update to 0.1.24

PR:		132527
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer

3 files changed, 571 insertions, 485 deletions

diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 7898e3dc3575..3ee0b3f99814 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	5.0.0
+PORTVERSION=	6.0.1
 RELEASE=	${PORTNAME:U}-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index d5738dcba86b..760dab2e11e9 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -1,3 +1,3 @@
-MD5 (emboss/EMBOSS-5.0.0.tar.gz) = be4c895220ad34afd65d450ba7d8e34b
-SHA256 (emboss/EMBOSS-5.0.0.tar.gz) = 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
-SIZE (emboss/EMBOSS-5.0.0.tar.gz) = 20666560
+MD5 (emboss/EMBOSS-6.0.1.tar.gz) = 2182b148dace6bea403deed8facae40d
+SHA256 (emboss/EMBOSS-6.0.1.tar.gz) = 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+SIZE (emboss/EMBOSS-6.0.1.tar.gz) = 20204153
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 6e48cfe6e406..bc0bb59e818d 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -5,6 +5,8 @@ bin/acdpretty
 bin/acdtable
 bin/acdtrace
 bin/acdvalid
+bin/aligncopy
+bin/aligncopypair
 bin/antigenic
 bin/backtranambig
 bin/backtranseq
@@ -22,6 +24,7 @@ bin/codcopy
 bin/coderet
 bin/compseq
 bin/cons
+bin/consambig
 bin/cpgplot
 bin/cpgreport
 bin/cusp
@@ -36,6 +39,7 @@ bin/dbxfasta
 bin/dbxflat
 bin/dbxgcg
 bin/degapseq
+bin/density
 bin/descseq
 bin/diffseq
 bin/digest
@@ -59,6 +63,8 @@ bin/etandem
 bin/extractalign
 bin/extractfeat
 bin/extractseq
+bin/featcopy
+bin/featreport
 bin/findkm
 bin/freak
 bin/fuzznuc
@@ -71,14 +77,20 @@ bin/helixturnhelix
 bin/hmoment
 bin/iep
 bin/infoalign
+bin/infobase
+bin/inforesidue
 bin/infoseq
 bin/isochore
+bin/jaspextract
+bin/jaspscan
 bin/jembossctl
 bin/lindna
 bin/listor
 bin/makenucseq
 bin/makeprotseq
 bin/marscan
+bin/maskambignuc
+bin/maskambigprot
 bin/maskfeat
 bin/maskseq
 bin/matcher
@@ -91,7 +103,10 @@ bin/needle
 bin/newcpgreport
 bin/newcpgseek
 bin/newseq
+bin/nohtml
 bin/noreturn
+bin/nospace
+bin/notab
 bin/notseq
 bin/nthseq
 bin/octanol
@@ -143,6 +158,8 @@ bin/sigcleave
 bin/silent
 bin/sirna
 bin/sixpack
+bin/sizeseq
+bin/skipredundant
 bin/skipseq
 bin/splitter
 bin/stretcher
@@ -159,6 +176,7 @@ bin/tranalign
 bin/transeq
 bin/trimest
 bin/trimseq
+bin/trimspace
 bin/twofeat
 bin/union
 bin/vectorstrip
@@ -188,6 +206,8 @@ 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
@@ -279,11 +299,11 @@ include/pcreposix.h
 lib/libajax.a
 lib/libajax.la
 lib/libajax.so
-lib/libajax.so.5
+lib/libajax.so.6
 lib/libajaxg.a
 lib/libajaxg.la
 lib/libajaxg.so
-lib/libajaxg.so.5
+lib/libajaxg.so.6
 lib/libeplplot.a
 lib/libeplplot.la
 lib/libeplplot.so
@@ -291,450 +311,7 @@ lib/libeplplot.so.5
 lib/libnucleus.a
 lib/libnucleus.la
 lib/libnucleus.so
-lib/libnucleus.so.5
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/aaindexextract.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/abiview.1.abiview.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/abiview.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acd_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdc.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdlog.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdpretty.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdtable.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdtrace.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdvalid.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/ajtest.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_differences_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_dot_plots_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_global_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_local_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_multiple_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/antigenic.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/backtranambig.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/backtranseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/banana.1.banana.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/banana.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/biosed.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/btwisted.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cai.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/chaos.1.chaos.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/chaos.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/charge.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/checktrans.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/chips.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cirdna.1.cirdna.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cirdna.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/codcmp.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/codcopy.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/coderet.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/compseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cons.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cpgplot.1.cpgplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cpgplot.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cusp.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cutgextract.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cutseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dan.2.dan.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dan.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbiblast.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbifasta.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbiflat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbigcg.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbxfasta.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbxflat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbxgcg.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/degapseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/descseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/diffseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/digest.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/display_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/distmat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotmatcher.1.dotmatcher.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotmatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotpath.1.dotpath.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotpath.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dottup.1.dottup.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dottup.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dreg.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/edialign.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/einverted.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emboss_icon.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emboss_icon.jpg
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/embossdata.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/embossversion.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emma.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emowse.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/entret.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/enzyme_kinetics_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/epestfind.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/eprimer3.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/equicktandem.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/est2genome.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/etandem.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/extractfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/extractseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/feature_tables_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/findkm.1.findkm.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/findkm.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/freak.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/fuzznuc.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/fuzzpro.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/fuzztran.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/garnier.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/geecee.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/getorf.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/groups.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/helixturnhelix.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/hmm_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/hmoment.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/iep.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/index.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/infoalign.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/information_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/infoseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/isochore.1.isochore.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/isochore.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/jembossctl.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/lindna.1.lindna.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/lindna.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/listor.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/makenucseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/makeprotseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/marscan.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/maskfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/maskseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/matcher.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/megamerger.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/menus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/merger.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/msbar.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/mwcontam.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/mwfilter.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/needle.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/newcpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/newcpgseek.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/newseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/noreturn.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/notseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nthseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_codon_usage_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_codon_usage_nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_cpg_islands_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_primers_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_repeats_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_restriction_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_transcription_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/nucleic_translation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/octanol.1.octanol.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/octanol.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/oddcomp.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/palindrome.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pasteseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/patmatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/patmatmotifs.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepcoil.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepinfo.1.pepinfo.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepinfo.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepnet.1.pepnet.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepnet.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepstats.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwheel.1.pepwheel.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwheel.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwindow.1.pepwindow.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwindow.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwindowall.1.pepwindowall.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwindowall.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_continuous_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_discrete_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_distance_matrix_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_gene_frequencies_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_molecular_sequence_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_tree_drawing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotcon.1.plotcon.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotcon.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotorf.1.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotorf.2.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotorf.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/polydot.1.polydot.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/polydot.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/preg.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyplot.1.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyplot.2.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyplot.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/primersearch.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/printsextract.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/profit.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prophecy.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prophet.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prosextract.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_3d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_sequence_alignment_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pscan.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/psiphi.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/rebaseextract.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/recoder.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/redata.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/remap.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/restover.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/restrict.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/revseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seealso.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seqret.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seqretsplit.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showalign.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showdb.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showorf.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/shuffleseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/sigcleave.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/silent.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/sirna.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/sixpack.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/skipseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/splitter.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/stretcher.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/stssearch.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/supermatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/syco.1.syco.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tcode.2.tcode.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tcode.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/template.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/test_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/textsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tfscan.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tmap.1.tmap.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tmap.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tranalign.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/transeq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/trimest.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/trimseq.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/twofeat.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/union.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/utils_database_creation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/utils_database_indexing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/water.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/whichdb.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wobble.1.wobble.gif
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wobble.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wordcount.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wordfinder.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wordmatch.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wossname.html
-%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/yank.html
-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdc.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdlog.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdpretty.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtable.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/antigenic.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranambig.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcopy.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cusp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutgextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiblast.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxfasta.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxflat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbxgcg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotmatcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotpath.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dottup.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dreg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edialign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/einverted.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossdata.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossversion.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emma.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emowse.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/entret.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epestfind.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprimer3.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/equicktandem.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/est2genome.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzznuc.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzzpro.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/makenucseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/makeprotseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/psiphi.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordfinder.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
+lib/libnucleus.so.6
 %%DATADIR%%/acd/aaindexextract.acd
 %%DATADIR%%/acd/abiview.acd
 %%DATADIR%%/acd/acdc.acd
@@ -746,6 +323,8 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/ajbad.acd
 %%DATADIR%%/acd/ajfeatest.acd
 %%DATADIR%%/acd/ajtest.acd
+%%DATADIR%%/acd/aligncopy.acd
+%%DATADIR%%/acd/aligncopypair.acd
 %%DATADIR%%/acd/antigenic.acd
 %%DATADIR%%/acd/backtranambig.acd
 %%DATADIR%%/acd/backtranseq.acd
@@ -765,6 +344,7 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/complex.acd
 %%DATADIR%%/acd/compseq.acd
 %%DATADIR%%/acd/cons.acd
+%%DATADIR%%/acd/consambig.acd
 %%DATADIR%%/acd/corbatest.acd
 %%DATADIR%%/acd/cpgplot.acd
 %%DATADIR%%/acd/cpgreport.acd
@@ -781,14 +361,7 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/dbxgcg.acd
 %%DATADIR%%/acd/dbxstat.acd
 %%DATADIR%%/acd/degapseq.acd
-%%DATADIR%%/acd/demoalign.acd
-%%DATADIR%%/acd/demofeatures.acd
-%%DATADIR%%/acd/demolist.acd
-%%DATADIR%%/acd/demoreport.acd
-%%DATADIR%%/acd/demosequence.acd
-%%DATADIR%%/acd/demostring.acd
-%%DATADIR%%/acd/demostringnew.acd
-%%DATADIR%%/acd/demotable.acd
+%%DATADIR%%/acd/density.acd
 %%DATADIR%%/acd/descseq.acd
 %%DATADIR%%/acd/diffseq.acd
 %%DATADIR%%/acd/digest.acd
@@ -813,6 +386,8 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/extractalign.acd
 %%DATADIR%%/acd/extractfeat.acd
 %%DATADIR%%/acd/extractseq.acd
+%%DATADIR%%/acd/featcopy.acd
+%%DATADIR%%/acd/featreport.acd
 %%DATADIR%%/acd/findkm.acd
 %%DATADIR%%/acd/freak.acd
 %%DATADIR%%/acd/fuzznuc.acd
@@ -831,6 +406,8 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/infoseq.acd
 %%DATADIR%%/acd/intconv.acd
 %%DATADIR%%/acd/isochore.acd
+%%DATADIR%%/acd/jaspextract.acd
+%%DATADIR%%/acd/jaspscan.acd
 %%DATADIR%%/acd/keywords.standard
 %%DATADIR%%/acd/knowntypes.standard
 %%DATADIR%%/acd/lindna.acd
@@ -838,6 +415,8 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/makenucseq.acd
 %%DATADIR%%/acd/makeprotseq.acd
 %%DATADIR%%/acd/marscan.acd
+%%DATADIR%%/acd/maskambignuc.acd
+%%DATADIR%%/acd/maskambigprot.acd
 %%DATADIR%%/acd/maskfeat.acd
 %%DATADIR%%/acd/maskseq.acd
 %%DATADIR%%/acd/matcher.acd
@@ -851,7 +430,10 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/newcpgreport.acd
 %%DATADIR%%/acd/newcpgseek.acd
 %%DATADIR%%/acd/newseq.acd
+%%DATADIR%%/acd/nohtml.acd
 %%DATADIR%%/acd/noreturn.acd
+%%DATADIR%%/acd/nospace.acd
+%%DATADIR%%/acd/notab.acd
 %%DATADIR%%/acd/notseq.acd
 %%DATADIR%%/acd/nthseq.acd
 %%DATADIR%%/acd/octanol.acd
@@ -914,6 +496,8 @@ lib/libnucleus.so.5
 %%DATADIR%%/acd/silent.acd
 %%DATADIR%%/acd/sirna.acd
 %%DATADIR%%/acd/sixpack.acd
+%%DATADIR%%/acd/sizeseq.acd
+%%DATADIR%%/acd/skipredundant.acd
 %%DATADIR%%/acd/skipseq.acd
 %%DATADIR%%/acd/splitter.acd
 %%DATADIR%%/acd/stretcher.acd
@@ -1301,6 +885,7 @@ lib/libnucleus.so.5
 %%DATADIR%%/data/Efeatures.emboss
 %%DATADIR%%/data/Efeatures.gff
 %%DATADIR%%/data/Efeatures.gff3
+%%DATADIR%%/data/Efeatures.gff3protein
 %%DATADIR%%/data/Efeatures.gffprotein
 %%DATADIR%%/data/Efeatures.pir
 %%DATADIR%%/data/Efeatures.protein
@@ -1312,6 +897,7 @@ lib/libnucleus.so.5
 %%DATADIR%%/data/Emass.dat
 %%DATADIR%%/data/Emassmod.dat
 %%DATADIR%%/data/Ememe.dat
+%%DATADIR%%/data/Emolwt.dat
 %%DATADIR%%/data/Emwfilter.dat
 %%DATADIR%%/data/Enakai.dat
 %%DATADIR%%/data/Epepcoil.dat
@@ -1319,6 +905,7 @@ lib/libnucleus.so.5
 %%DATADIR%%/data/Epprofile
 %%DATADIR%%/data/Eprior1.plib
 %%DATADIR%%/data/Eprior30.plib
+%%DATADIR%%/data/Eresidues.iub
 %%DATADIR%%/data/Erna.melt
 %%DATADIR%%/data/Esig.euk
 %%DATADIR%%/data/Esig.pro
@@ -1333,6 +920,12 @@ lib/libnucleus.so.5
 %%DATADIR%%/data/Etcode.dat
 %%DATADIR%%/data/Evdw.dat
 %%DATADIR%%/data/Ewhite-wimley.dat
+%%DATADIR%%/data/JASPAR_CNE/dummyfile
+%%DATADIR%%/data/JASPAR_CORE/dummyfile
+%%DATADIR%%/data/JASPAR_FAM/dummyfile
+%%DATADIR%%/data/JASPAR_PHYLOFACTS/dummyfile
+%%DATADIR%%/data/JASPAR_POLII/dummyfile
+%%DATADIR%%/data/JASPAR_SPLICE/dummyfile
 %%DATADIR%%/data/Matrices.nucleotide
 %%DATADIR%%/data/Matrices.protein
 %%DATADIR%%/data/Matrices.proteinstructure
@@ -1344,6 +937,494 @@ lib/libnucleus.so.5
 %%DATADIR%%/data/tp400_dna
 %%DATADIR%%/data/tp400_prot
 %%DATADIR%%/data/tp400_trans
+%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
+%%DOCSDIR%%/manuals/admin.aux
+%%DOCSDIR%%/manuals/admin.dvi
+%%DOCSDIR%%/manuals/admin.log
+%%DOCSDIR%%/manuals/admin.pdf
+%%DOCSDIR%%/manuals/admin.ps
+%%DOCSDIR%%/manuals/admin.tex
+%%DOCSDIR%%/manuals/admin.toc
+%%DOCSDIR%%/manuals/adminguide.tar.gz
+%%DOCSDIR%%/manuals/domainatrix.doc
+%%DOCSDIR%%/manuals/emboss.sty
+%%DOCSDIR%%/manuals/emboss_qg.pdf
+%%DOCSDIR%%/manuals/emboss_qg.ps
+%%DOCSDIR%%/manuals/fdl.txt
+%%DOCSDIR%%/manuals/program.ps.gz
+%%DOCSDIR%%/programs/html/aaindexextract.html
+%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
+%%DOCSDIR%%/programs/html/abiview.html
+%%DOCSDIR%%/programs/html/acd_group.html
+%%DOCSDIR%%/programs/html/acdc.html
+%%DOCSDIR%%/programs/html/acdlog.html
+%%DOCSDIR%%/programs/html/acdpretty.html
+%%DOCSDIR%%/programs/html/acdtable.html
+%%DOCSDIR%%/programs/html/acdtrace.html
+%%DOCSDIR%%/programs/html/acdvalid.html
+%%DOCSDIR%%/programs/html/ajtest.html
+%%DOCSDIR%%/programs/html/aligncopy.html
+%%DOCSDIR%%/programs/html/aligncopypair.html
+%%DOCSDIR%%/programs/html/alignment_consensus_group.html
+%%DOCSDIR%%/programs/html/alignment_differences_group.html
+%%DOCSDIR%%/programs/html/alignment_dot_plots_group.html
+%%DOCSDIR%%/programs/html/alignment_global_group.html
+%%DOCSDIR%%/programs/html/alignment_local_group.html
+%%DOCSDIR%%/programs/html/alignment_multiple_group.html
+%%DOCSDIR%%/programs/html/antigenic.html
+%%DOCSDIR%%/programs/html/assembly_fragment_assembly_group.html
+%%DOCSDIR%%/programs/html/backtranambig.html
+%%DOCSDIR%%/programs/html/backtranseq.html
+%%DOCSDIR%%/programs/html/banana.1.banana.gif
+%%DOCSDIR%%/programs/html/banana.html
+%%DOCSDIR%%/programs/html/biosed.html
+%%DOCSDIR%%/programs/html/btwisted.html
+%%DOCSDIR%%/programs/html/cai.html
+%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
+%%DOCSDIR%%/programs/html/chaos.html
+%%DOCSDIR%%/programs/html/charge.html
+%%DOCSDIR%%/programs/html/checktrans.html
+%%DOCSDIR%%/programs/html/chips.html
+%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
+%%DOCSDIR%%/programs/html/cirdna.html
+%%DOCSDIR%%/programs/html/codcmp.html
+%%DOCSDIR%%/programs/html/codcopy.html
+%%DOCSDIR%%/programs/html/coderet.html
+%%DOCSDIR%%/programs/html/complex.html
+%%DOCSDIR%%/programs/html/compseq.html
+%%DOCSDIR%%/programs/html/cons.html
+%%DOCSDIR%%/programs/html/consambig.html
+%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
+%%DOCSDIR%%/programs/html/cpgplot.html
+%%DOCSDIR%%/programs/html/cpgreport.html
+%%DOCSDIR%%/programs/html/cusp.html
+%%DOCSDIR%%/programs/html/cutgextract.html
+%%DOCSDIR%%/programs/html/cutseq.html
+%%DOCSDIR%%/programs/html/dan.2.dan.gif
+%%DOCSDIR%%/programs/html/dan.html
+%%DOCSDIR%%/programs/html/dbiblast.html
+%%DOCSDIR%%/programs/html/dbifasta.html
+%%DOCSDIR%%/programs/html/dbiflat.html
+%%DOCSDIR%%/programs/html/dbigcg.html
+%%DOCSDIR%%/programs/html/dbxfasta.html
+%%DOCSDIR%%/programs/html/dbxflat.html
+%%DOCSDIR%%/programs/html/dbxgcg.html
+%%DOCSDIR%%/programs/html/degapseq.html
+%%DOCSDIR%%/programs/html/density.html
+%%DOCSDIR%%/programs/html/descseq.html
+%%DOCSDIR%%/programs/html/diffseq.html
+%%DOCSDIR%%/programs/html/digest.html
+%%DOCSDIR%%/programs/html/display_group.html
+%%DOCSDIR%%/programs/html/distmat.html
+%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
+%%DOCSDIR%%/programs/html/dotmatcher.html
+%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
+%%DOCSDIR%%/programs/html/dotpath.html
+%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
+%%DOCSDIR%%/programs/html/dottup.html
+%%DOCSDIR%%/programs/html/dreg.html
+%%DOCSDIR%%/programs/html/edialign.html
+%%DOCSDIR%%/programs/html/edit_group.html
+%%DOCSDIR%%/programs/html/einverted.html
+%%DOCSDIR%%/programs/html/emboss_icon.gif
+%%DOCSDIR%%/programs/html/emboss_icon.jpg
+%%DOCSDIR%%/programs/html/embossdata.html
+%%DOCSDIR%%/programs/html/embossversion.html
+%%DOCSDIR%%/programs/html/emma.html
+%%DOCSDIR%%/programs/html/emowse.html
+%%DOCSDIR%%/programs/html/entret.html
+%%DOCSDIR%%/programs/html/enzyme_kinetics_group.html
+%%DOCSDIR%%/programs/html/epestfind.1.epestfind.gif
+%%DOCSDIR%%/programs/html/epestfind.html
+%%DOCSDIR%%/programs/html/eprimer3.html
+%%DOCSDIR%%/programs/html/equicktandem.html
+%%DOCSDIR%%/programs/html/est2genome.html
+%%DOCSDIR%%/programs/html/etandem.html
+%%DOCSDIR%%/programs/html/extractalign.html
+%%DOCSDIR%%/programs/html/extractfeat.html
+%%DOCSDIR%%/programs/html/extractseq.html
+%%DOCSDIR%%/programs/html/featcopy.html
+%%DOCSDIR%%/programs/html/featreport.html
+%%DOCSDIR%%/programs/html/feature_tables_group.html
+%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
+%%DOCSDIR%%/programs/html/findkm.html
+%%DOCSDIR%%/programs/html/freak.html
+%%DOCSDIR%%/programs/html/fuzznuc.html
+%%DOCSDIR%%/programs/html/fuzzpro.html
+%%DOCSDIR%%/programs/html/fuzztran.html
+%%DOCSDIR%%/programs/html/garnier.html
+%%DOCSDIR%%/programs/html/geecee.html
+%%DOCSDIR%%/programs/html/getorf.html
+%%DOCSDIR%%/programs/html/groups.html
+%%DOCSDIR%%/programs/html/helixturnhelix.html
+%%DOCSDIR%%/programs/html/hmm_group.html
+%%DOCSDIR%%/programs/html/hmoment.html
+%%DOCSDIR%%/programs/html/iep.html
+%%DOCSDIR%%/programs/html/index.html
+%%DOCSDIR%%/programs/html/infoalign.html
+%%DOCSDIR%%/programs/html/infobase.html
+%%DOCSDIR%%/programs/html/inforesidue.html
+%%DOCSDIR%%/programs/html/information_group.html
+%%DOCSDIR%%/programs/html/infoseq.html
+%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
+%%DOCSDIR%%/programs/html/isochore.html
+%%DOCSDIR%%/programs/html/jaspextract.html
+%%DOCSDIR%%/programs/html/jaspscan.html
+%%DOCSDIR%%/programs/html/jembossctl.html
+%%DOCSDIR%%/programs/html/libscan.html
+%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
+%%DOCSDIR%%/programs/html/lindna.html
+%%DOCSDIR%%/programs/html/listor.html
+%%DOCSDIR%%/programs/html/makenucseq.html
+%%DOCSDIR%%/programs/html/makeprotseq.html
+%%DOCSDIR%%/programs/html/marscan.html
+%%DOCSDIR%%/programs/html/maskambignuc.html
+%%DOCSDIR%%/programs/html/maskambigprot.html
+%%DOCSDIR%%/programs/html/maskfeat.html
+%%DOCSDIR%%/programs/html/maskseq.html
+%%DOCSDIR%%/programs/html/matcher.html
+%%DOCSDIR%%/programs/html/megamerger.html
+%%DOCSDIR%%/programs/html/menus_group.html
+%%DOCSDIR%%/programs/html/merger.html
+%%DOCSDIR%%/programs/html/msbar.html
+%%DOCSDIR%%/programs/html/mwcontam.html
+%%DOCSDIR%%/programs/html/mwfilter.html
+%%DOCSDIR%%/programs/html/needle.html
+%%DOCSDIR%%/programs/html/newcpgreport.html
+%%DOCSDIR%%/programs/html/newcpgseek.html
+%%DOCSDIR%%/programs/html/newseq.html
+%%DOCSDIR%%/programs/html/nohtml.html
+%%DOCSDIR%%/programs/html/noreturn.html
+%%DOCSDIR%%/programs/html/nospace.html
+%%DOCSDIR%%/programs/html/notab.html
+%%DOCSDIR%%/programs/html/notseq.html
+%%DOCSDIR%%/programs/html/nthseq.html
+%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
+%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
+%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
+%%DOCSDIR%%/programs/html/nucleic_composition_group.html
+%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
+%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
+%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
+%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
+%%DOCSDIR%%/programs/html/nucleic_primers_group.html
+%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
+%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
+%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
+%%DOCSDIR%%/programs/html/nucleic_rna_folding_group.html
+%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
+%%DOCSDIR%%/programs/html/nucleic_translation_group.html
+%%DOCSDIR%%/programs/html/octanol.1.octanol.gif
+%%DOCSDIR%%/programs/html/octanol.html
+%%DOCSDIR%%/programs/html/oddcomp.html
+%%DOCSDIR%%/programs/html/palindrome.html
+%%DOCSDIR%%/programs/html/pasteseq.html
+%%DOCSDIR%%/programs/html/patmatdb.html
+%%DOCSDIR%%/programs/html/patmatmotifs.html
+%%DOCSDIR%%/programs/html/pepcoil.html
+%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif
+%%DOCSDIR%%/programs/html/pepinfo.html
+%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif
+%%DOCSDIR%%/programs/html/pepnet.html
+%%DOCSDIR%%/programs/html/pepstats.html
+%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif
+%%DOCSDIR%%/programs/html/pepwheel.html
+%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif
+%%DOCSDIR%%/programs/html/pepwindow.html
+%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif
+%%DOCSDIR%%/programs/html/pepwindowall.html
+%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
+%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
+%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
+%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
+%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
+%%DOCSDIR%%/programs/html/phylogeny_group.html
+%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
+%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
+%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
+%%DOCSDIR%%/programs/html/plotcon.html
+%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
+%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
+%%DOCSDIR%%/programs/html/plotorf.html
+%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
+%%DOCSDIR%%/programs/html/polydot.html
+%%DOCSDIR%%/programs/html/preg.html
+%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
+%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
+%%DOCSDIR%%/programs/html/prettyplot.html
+%%DOCSDIR%%/programs/html/prettyseq.html
+%%DOCSDIR%%/programs/html/primersearch.html
+%%DOCSDIR%%/programs/html/printsextract.html
+%%DOCSDIR%%/programs/html/profit.html
+%%DOCSDIR%%/programs/html/prophecy.html
+%%DOCSDIR%%/programs/html/prophet.html
+%%DOCSDIR%%/programs/html/prosextract.html
+%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
+%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
+%%DOCSDIR%%/programs/html/protein_composition_group.html
+%%DOCSDIR%%/programs/html/protein_motifs_group.html
+%%DOCSDIR%%/programs/html/protein_mutation_group.html
+%%DOCSDIR%%/programs/html/protein_profiles_group.html
+%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
+%%DOCSDIR%%/programs/html/pscan.html
+%%DOCSDIR%%/programs/html/psiphi.html
+%%DOCSDIR%%/programs/html/rebaseextract.html
+%%DOCSDIR%%/programs/html/recoder.html
+%%DOCSDIR%%/programs/html/redata.html
+%%DOCSDIR%%/programs/html/remap.html
+%%DOCSDIR%%/programs/html/restover.html
+%%DOCSDIR%%/programs/html/restrict.html
+%%DOCSDIR%%/programs/html/revseq.html
+%%DOCSDIR%%/programs/html/seealso.html
+%%DOCSDIR%%/programs/html/seqmatchall.html
+%%DOCSDIR%%/programs/html/seqret.html
+%%DOCSDIR%%/programs/html/seqretsplit.html
+%%DOCSDIR%%/programs/html/showalign.html
+%%DOCSDIR%%/programs/html/showdb.html
+%%DOCSDIR%%/programs/html/showfeat.html
+%%DOCSDIR%%/programs/html/showorf.html
+%%DOCSDIR%%/programs/html/showseq.html
+%%DOCSDIR%%/programs/html/shuffleseq.html
+%%DOCSDIR%%/programs/html/sigcleave.html
+%%DOCSDIR%%/programs/html/silent.html
+%%DOCSDIR%%/programs/html/sirna.html
+%%DOCSDIR%%/programs/html/sixpack.html
+%%DOCSDIR%%/programs/html/sizeseq.html
+%%DOCSDIR%%/programs/html/skipredundant.html
+%%DOCSDIR%%/programs/html/skipseq.html
+%%DOCSDIR%%/programs/html/splitter.html
+%%DOCSDIR%%/programs/html/stretcher.html
+%%DOCSDIR%%/programs/html/stssearch.html
+%%DOCSDIR%%/programs/html/supermatcher.html
+%%DOCSDIR%%/programs/html/syco.1.syco.gif
+%%DOCSDIR%%/programs/html/syco.html
+%%DOCSDIR%%/programs/html/tcode.2.tcode.gif
+%%DOCSDIR%%/programs/html/tcode.html
+%%DOCSDIR%%/programs/html/template.html
+%%DOCSDIR%%/programs/html/test_group.html
+%%DOCSDIR%%/programs/html/textsearch.html
+%%DOCSDIR%%/programs/html/tfextract.html
+%%DOCSDIR%%/programs/html/tfm.html
+%%DOCSDIR%%/programs/html/tfscan.html
+%%DOCSDIR%%/programs/html/tmap.1.tmap.gif
+%%DOCSDIR%%/programs/html/tmap.html
+%%DOCSDIR%%/programs/html/tranalign.html
+%%DOCSDIR%%/programs/html/transeq.html
+%%DOCSDIR%%/programs/html/trimest.html
+%%DOCSDIR%%/programs/html/trimseq.html
+%%DOCSDIR%%/programs/html/trimspace.html
+%%DOCSDIR%%/programs/html/twofeat.html
+%%DOCSDIR%%/programs/html/union.html
+%%DOCSDIR%%/programs/html/utils_database_creation_group.html
+%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
+%%DOCSDIR%%/programs/html/utils_misc_group.html
+%%DOCSDIR%%/programs/html/vectorstrip.html
+%%DOCSDIR%%/programs/html/water.html
+%%DOCSDIR%%/programs/html/whichdb.html
+%%DOCSDIR%%/programs/html/wobble.1.wobble.gif
+%%DOCSDIR%%/programs/html/wobble.html
+%%DOCSDIR%%/programs/html/wordcount.html
+%%DOCSDIR%%/programs/html/wordfinder.html
+%%DOCSDIR%%/programs/html/wordmatch.html
+%%DOCSDIR%%/programs/html/wossname.html
+%%DOCSDIR%%/programs/html/yank.html
+%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt
+%%DOCSDIR%%/programs/text/aaindexextract.txt
+%%DOCSDIR%%/programs/text/abiview.txt
+%%DOCSDIR%%/programs/text/acdc.txt
+%%DOCSDIR%%/programs/text/acdlog.txt
+%%DOCSDIR%%/programs/text/acdpretty.txt
+%%DOCSDIR%%/programs/text/acdtable.txt
+%%DOCSDIR%%/programs/text/acdtrace.txt
+%%DOCSDIR%%/programs/text/acdvalid.txt
+%%DOCSDIR%%/programs/text/aligncopy.txt
+%%DOCSDIR%%/programs/text/aligncopypair.txt
+%%DOCSDIR%%/programs/text/antigenic.txt
+%%DOCSDIR%%/programs/text/backtranambig.txt
+%%DOCSDIR%%/programs/text/backtranseq.txt
+%%DOCSDIR%%/programs/text/banana.txt
+%%DOCSDIR%%/programs/text/biosed.txt
+%%DOCSDIR%%/programs/text/btwisted.txt
+%%DOCSDIR%%/programs/text/cai.txt
+%%DOCSDIR%%/programs/text/chaos.txt
+%%DOCSDIR%%/programs/text/charge.txt
+%%DOCSDIR%%/programs/text/checktrans.txt
+%%DOCSDIR%%/programs/text/chips.txt
+%%DOCSDIR%%/programs/text/cirdna.txt
+%%DOCSDIR%%/programs/text/codcmp.txt
+%%DOCSDIR%%/programs/text/codcopy.txt
+%%DOCSDIR%%/programs/text/coderet.txt
+%%DOCSDIR%%/programs/text/complex.txt
+%%DOCSDIR%%/programs/text/compseq.txt
+%%DOCSDIR%%/programs/text/cons.txt
+%%DOCSDIR%%/programs/text/consambig.txt
+%%DOCSDIR%%/programs/text/cpgplot.txt
+%%DOCSDIR%%/programs/text/cpgreport.txt
+%%DOCSDIR%%/programs/text/cusp.txt
+%%DOCSDIR%%/programs/text/cutgextract.txt
+%%DOCSDIR%%/programs/text/cutseq.txt
+%%DOCSDIR%%/programs/text/dan.txt
+%%DOCSDIR%%/programs/text/dbiblast.txt
+%%DOCSDIR%%/programs/text/dbifasta.txt
+%%DOCSDIR%%/programs/text/dbiflat.txt
+%%DOCSDIR%%/programs/text/dbigcg.txt
+%%DOCSDIR%%/programs/text/dbxfasta.txt
+%%DOCSDIR%%/programs/text/dbxflat.txt
+%%DOCSDIR%%/programs/text/dbxgcg.txt
+%%DOCSDIR%%/programs/text/degapseq.txt
+%%DOCSDIR%%/programs/text/density.txt
+%%DOCSDIR%%/programs/text/descseq.txt
+%%DOCSDIR%%/programs/text/diffseq.txt
+%%DOCSDIR%%/programs/text/digest.txt
+%%DOCSDIR%%/programs/text/distmat.txt
+%%DOCSDIR%%/programs/text/dotmatcher.txt
+%%DOCSDIR%%/programs/text/dotpath.txt
+%%DOCSDIR%%/programs/text/dottup.txt
+%%DOCSDIR%%/programs/text/dreg.txt
+%%DOCSDIR%%/programs/text/edialign.txt
+%%DOCSDIR%%/programs/text/einverted.txt
+%%DOCSDIR%%/programs/text/embossdata.txt
+%%DOCSDIR%%/programs/text/embossversion.txt
+%%DOCSDIR%%/programs/text/emma.txt
+%%DOCSDIR%%/programs/text/emowse.txt
+%%DOCSDIR%%/programs/text/entret.txt
+%%DOCSDIR%%/programs/text/epestfind.txt
+%%DOCSDIR%%/programs/text/eprimer3.txt
+%%DOCSDIR%%/programs/text/equicktandem.txt
+%%DOCSDIR%%/programs/text/est2genome.txt
+%%DOCSDIR%%/programs/text/etandem.txt
+%%DOCSDIR%%/programs/text/extractalign.txt
+%%DOCSDIR%%/programs/text/extractfeat.txt
+%%DOCSDIR%%/programs/text/extractseq.txt
+%%DOCSDIR%%/programs/text/featcopy.txt
+%%DOCSDIR%%/programs/text/featreport.txt
+%%DOCSDIR%%/programs/text/findkm.txt
+%%DOCSDIR%%/programs/text/freak.txt
+%%DOCSDIR%%/programs/text/frestdist.txt
+%%DOCSDIR%%/programs/text/fuzznuc.txt
+%%DOCSDIR%%/programs/text/fuzzpro.txt
+%%DOCSDIR%%/programs/text/fuzztran.txt
+%%DOCSDIR%%/programs/text/garnier.txt
+%%DOCSDIR%%/programs/text/geecee.txt
+%%DOCSDIR%%/programs/text/getorf.txt
+%%DOCSDIR%%/programs/text/helixturnhelix.txt
+%%DOCSDIR%%/programs/text/hmoment.txt
+%%DOCSDIR%%/programs/text/iep.txt
+%%DOCSDIR%%/programs/text/infoalign.txt
+%%DOCSDIR%%/programs/text/infobase.txt
+%%DOCSDIR%%/programs/text/inforesidue.txt
+%%DOCSDIR%%/programs/text/infoseq.txt
+%%DOCSDIR%%/programs/text/isochore.txt
+%%DOCSDIR%%/programs/text/jaspextract.txt
+%%DOCSDIR%%/programs/text/jaspscan.txt
+%%DOCSDIR%%/programs/text/jembossctl.txt
+%%DOCSDIR%%/programs/text/lindna.txt
+%%DOCSDIR%%/programs/text/listor.txt
+%%DOCSDIR%%/programs/text/makenucseq.txt
+%%DOCSDIR%%/programs/text/makeprotseq.txt
+%%DOCSDIR%%/programs/text/marscan.txt
+%%DOCSDIR%%/programs/text/maskambignuc.txt
+%%DOCSDIR%%/programs/text/maskambigprot.txt
+%%DOCSDIR%%/programs/text/maskfeat.txt
+%%DOCSDIR%%/programs/text/maskseq.txt
+%%DOCSDIR%%/programs/text/matcher.txt
+%%DOCSDIR%%/programs/text/megamerger.txt
+%%DOCSDIR%%/programs/text/merger.txt
+%%DOCSDIR%%/programs/text/msbar.txt
+%%DOCSDIR%%/programs/text/mwcontam.txt
+%%DOCSDIR%%/programs/text/mwfilter.txt
+%%DOCSDIR%%/programs/text/needle.txt
+%%DOCSDIR%%/programs/text/newcpgreport.txt
+%%DOCSDIR%%/programs/text/newcpgseek.txt
+%%DOCSDIR%%/programs/text/newseq.txt
+%%DOCSDIR%%/programs/text/nohtml.txt
+%%DOCSDIR%%/programs/text/noreturn.txt
+%%DOCSDIR%%/programs/text/nospace.txt
+%%DOCSDIR%%/programs/text/notab.txt
+%%DOCSDIR%%/programs/text/notseq.txt
+%%DOCSDIR%%/programs/text/nthseq.txt
+%%DOCSDIR%%/programs/text/octanol.txt
+%%DOCSDIR%%/programs/text/oddcomp.txt
+%%DOCSDIR%%/programs/text/palindrome.txt
+%%DOCSDIR%%/programs/text/pasteseq.txt
+%%DOCSDIR%%/programs/text/patmatdb.txt
+%%DOCSDIR%%/programs/text/patmatmotifs.txt
+%%DOCSDIR%%/programs/text/pepcoil.txt
+%%DOCSDIR%%/programs/text/pepinfo.txt
+%%DOCSDIR%%/programs/text/pepnet.txt
+%%DOCSDIR%%/programs/text/pepstats.txt
+%%DOCSDIR%%/programs/text/pepwheel.txt
+%%DOCSDIR%%/programs/text/pepwindow.txt
+%%DOCSDIR%%/programs/text/pepwindowall.txt
+%%DOCSDIR%%/programs/text/plotcon.txt
+%%DOCSDIR%%/programs/text/plotorf.txt
+%%DOCSDIR%%/programs/text/polydot.txt
+%%DOCSDIR%%/programs/text/preg.txt
+%%DOCSDIR%%/programs/text/prettyplot.txt
+%%DOCSDIR%%/programs/text/prettyseq.txt
+%%DOCSDIR%%/programs/text/primersearch.txt
+%%DOCSDIR%%/programs/text/printsextract.txt
+%%DOCSDIR%%/programs/text/profit.txt
+%%DOCSDIR%%/programs/text/prophecy.txt
+%%DOCSDIR%%/programs/text/prophet.txt
+%%DOCSDIR%%/programs/text/prosextract.txt
+%%DOCSDIR%%/programs/text/pscan.txt
+%%DOCSDIR%%/programs/text/psiphi.txt
+%%DOCSDIR%%/programs/text/rebaseextract.txt
+%%DOCSDIR%%/programs/text/recoder.txt
+%%DOCSDIR%%/programs/text/redata.txt
+%%DOCSDIR%%/programs/text/remap.txt
+%%DOCSDIR%%/programs/text/restover.txt
+%%DOCSDIR%%/programs/text/restrict.txt
+%%DOCSDIR%%/programs/text/revseq.txt
+%%DOCSDIR%%/programs/text/seealso.txt
+%%DOCSDIR%%/programs/text/seqmatchall.txt
+%%DOCSDIR%%/programs/text/seqret.txt
+%%DOCSDIR%%/programs/text/seqretsplit.txt
+%%DOCSDIR%%/programs/text/showalign.txt
+%%DOCSDIR%%/programs/text/showdb.txt
+%%DOCSDIR%%/programs/text/showfeat.txt
+%%DOCSDIR%%/programs/text/showorf.txt
+%%DOCSDIR%%/programs/text/showseq.txt
+%%DOCSDIR%%/programs/text/shuffleseq.txt
+%%DOCSDIR%%/programs/text/sigcleave.txt
+%%DOCSDIR%%/programs/text/silent.txt
+%%DOCSDIR%%/programs/text/sirna.txt
+%%DOCSDIR%%/programs/text/sixpack.txt
+%%DOCSDIR%%/programs/text/sizeseq.txt
+%%DOCSDIR%%/programs/text/skipredundant.txt
+%%DOCSDIR%%/programs/text/skipseq.txt
+%%DOCSDIR%%/programs/text/splitter.txt
+%%DOCSDIR%%/programs/text/stretcher.txt
+%%DOCSDIR%%/programs/text/stssearch.txt
+%%DOCSDIR%%/programs/text/supermatcher.txt
+%%DOCSDIR%%/programs/text/syco.txt
+%%DOCSDIR%%/programs/text/tcode.txt
+%%DOCSDIR%%/programs/text/textsearch.txt
+%%DOCSDIR%%/programs/text/tfextract.txt
+%%DOCSDIR%%/programs/text/tfm.txt
+%%DOCSDIR%%/programs/text/tfscan.txt
+%%DOCSDIR%%/programs/text/tmap.txt
+%%DOCSDIR%%/programs/text/tranalign.txt
+%%DOCSDIR%%/programs/text/transeq.txt
+%%DOCSDIR%%/programs/text/trimest.txt
+%%DOCSDIR%%/programs/text/trimseq.txt
+%%DOCSDIR%%/programs/text/trimspace.txt
+%%DOCSDIR%%/programs/text/twofeat.txt
+%%DOCSDIR%%/programs/text/union.txt
+%%DOCSDIR%%/programs/text/vectorstrip.txt
+%%DOCSDIR%%/programs/text/water.txt
+%%DOCSDIR%%/programs/text/whichdb.txt
+%%DOCSDIR%%/programs/text/wobble.txt
+%%DOCSDIR%%/programs/text/wordcount.txt
+%%DOCSDIR%%/programs/text/wordfinder.txt
+%%DOCSDIR%%/programs/text/wordmatch.txt
+%%DOCSDIR%%/programs/text/wossname.txt
+%%DOCSDIR%%/programs/text/yank.txt
+%%DOCSDIR%%/tutorials/emboss-gcg.ppt
+%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
+%%DOCSDIR%%/tutorials/emboss-talk.ppt
+%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
 %%DATADIR%%/emboss.default.template
 %%DATADIR%%/jemboss/LICENSE
 %%DATADIR%%/jemboss/README
@@ -1644,6 +1725,8 @@ lib/libnucleus.so.5
 %%DATADIR%%/test/data/nucseq.pat
 %%DATADIR%%/test/data/nucsimple.pat
 %%DATADIR%%/test/data/opsd.msf
+%%DATADIR%%/test/data/paamir.gff
+%%DATADIR%%/test/data/paamir.gff3
 %%DATADIR%%/test/data/paamir.pep
 %%DATADIR%%/test/data/pax6_cdna.fasta
 %%DATADIR%%/test/data/prints.test
@@ -1783,31 +1866,29 @@ lib/libnucleus.so.5
 %%DATADIR%%/test/testdb/division.lkp
 %%DATADIR%%/test/testdb/entrynam.idx
 %%DATADIR%%/test/testdb/testdb.fasta
+@dirrm bin
 @dirrm include/eplplot
 @dirrm include
+@dirrm lib
 @dirrm %%DATADIR%%/acd
-@dirrmtry %%DATADIR%%/data/AAINDEX
-@dirrmtry %%DATADIR%%/data/CODONS
-@dirrmtry %%DATADIR%%/data/REBASE
-@dirrmtry %%DATADIR%%/data/PRINTS
-@dirrmtry %%DATADIR%%/data/PROSITE
-@dirrmtry %%DATADIR%%/data
-@dirrm %%DATADIR%%/test/data
-@dirrm %%DATADIR%%/test/embl
-@dirrm %%DATADIR%%/test/genbank
-@dirrm %%DATADIR%%/test/pir
-@dirrm %%DATADIR%%/test/swiss
-@dirrm %%DATADIR%%/test/swnew
-@dirrm %%DATADIR%%/test/testdb
-@dirrm %%DATADIR%%/test
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/html/emboss/apps
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/html/emboss
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%DATADIR%%/data/AAINDEX
+@dirrm %%DATADIR%%/data/CODONS
+@dirrm %%DATADIR%%/data/JASPAR_CNE
+@dirrm %%DATADIR%%/data/JASPAR_CORE
+@dirrm %%DATADIR%%/data/JASPAR_FAM
+@dirrm %%DATADIR%%/data/JASPAR_PHYLOFACTS
+@dirrm %%DATADIR%%/data/JASPAR_POLII
+@dirrm %%DATADIR%%/data/JASPAR_SPLICE
+@dirrm %%DATADIR%%/data/PRINTS
+@dirrm %%DATADIR%%/data/PROSITE
+@dirrm %%DATADIR%%/data/REBASE
+@dirrm %%DATADIR%%/data
+@dirrm %%DOCSDIR%%/manuals
+@dirrm %%DOCSDIR%%/programs/html
+@dirrm %%DOCSDIR%%/programs/text
+@dirrm %%DOCSDIR%%/programs
+@dirrm %%DOCSDIR%%/tutorials
+@dirrm %%DOCSDIR%%
 @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree
 @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form
 @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
@@ -1824,8 +1905,8 @@ lib/libnucleus.so.5
 @dirrm %%DATADIR%%/jemboss/images
 @dirrm %%DATADIR%%/jemboss/lib/axis
 @dirrm %%DATADIR%%/jemboss/lib
-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
 @dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw
+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor
 @dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics
 @dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree
 @dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form
@@ -1843,8 +1924,13 @@ lib/libnucleus.so.5
 @dirrm %%DATADIR%%/jemboss/resources
 @dirrm %%DATADIR%%/jemboss/utils
 @dirrm %%DATADIR%%/jemboss
-@dirrmtry %%DATADIR%%
-@dirrmtry bin
-@dirrmtry include
-@dirrmtry lib
+@dirrm %%DATADIR%%/test/data
+@dirrm %%DATADIR%%/test/embl
+@dirrm %%DATADIR%%/test/genbank
+@dirrm %%DATADIR%%/test/pir
+@dirrm %%DATADIR%%/test/swiss
+@dirrm %%DATADIR%%/test/swnew
+@dirrm %%DATADIR%%/test/testdb
+@dirrm %%DATADIR%%/test
+@dirrm %%DATADIR%%
 @dirrmtry share