diff -ruN --exclude=CVS /usr/ports/biology/emboss/Makefile emboss/Makefile
--- /usr/ports/biology/emboss/Makefile	2008-03-24 11:54:11.000000000 -0300
+++ emboss/Makefile	2008-04-05 10:25:43.000000000 -0300
@@ -6,26 +6,20 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	3.0.0
-PORTREVISION=	2
+PORTVERSION=	5.0.0
+RELEASE=	${PORTNAME:U}-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
-		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
-		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
-DISTNAME=	${PORTNAME:U}-${PORTVERSION}
-DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
+DISTNAME=	${RELEASE}
+DISTFILES=	${RELEASE}${EXTRACT_SUFX}
 DIST_SUBDIR=	${PORTNAME}
 
-PATCH_WRKSRC=	${WRKDIR}
-
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of open source tools for genetic sequence analysis
 
 BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
 		primer3:${PORTSDIR}/biology/primer3
-LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
-		png.5:${PORTSDIR}/graphics/png
 
 CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*
 
@@ -40,21 +34,22 @@
 SUB_FILES=	pkg-message
 SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
 
-DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
+DOCSDIR=	${PREFIX}/share/${PORTNAME:U}/doc
 DATADIR=	${PREFIX}/share/${PORTNAME:U}
 
-DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
-CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
+CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}
 
-post-patch:
-.if !defined(NOPORTDOCS)
-.for DIR in ${DOC_DIRS}
-	@ ${REINPLACE_CMD} -e \
-	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
-	  ${WRKSRC}/${DIR}/Makefile.in
-.endfor
+.if defined(WITHOUT_X11)
+USE_XLIB=	yes
+USE_MOTIF=	yes
+LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
+		png.5:${PORTSDIR}/graphics/png
+CONFIGURE_ARGS+= --without-x
 .endif
 
+DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
+CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
+
 pre-install:
 	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
 
diff -ruN --exclude=CVS /usr/ports/biology/emboss/distinfo emboss/distinfo
--- /usr/ports/biology/emboss/distinfo	2006-03-31 06:43:20.000000000 -0300
+++ emboss/distinfo	2008-04-05 10:18:24.000000000 -0300
@@ -1,3 +1,3 @@
-MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
-SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
-SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
+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
diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-descr emboss/pkg-descr
--- /usr/ports/biology/emboss/pkg-descr	2001-08-03 08:32:41.000000000 -0300
+++ emboss/pkg-descr	2008-04-05 10:18:24.000000000 -0300
@@ -12,12 +12,8 @@
 
 EMBASSY packages are third party applications which have been integrated with
 the EMBOSS suite, but which are not included in the base EMBOSS distribution
-for licensing or other reasons.  This port includes the currently available
-EMBASSY applications.  During an interactive install the user will be asked
-to choose which of these will be installed (default: all).  Note that the
-EMBASSY versions of PHYLIP and HMMER should not clash with the standalone
-versions (also in ports/biology) due to the fact that their binaries have been
-renamed.
+for licensing or other reasons. The EMBASSY packages live in the
+biology/embassy port. 
 
 WWW: http://www.emboss.org/
 
diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist
--- /usr/ports/biology/emboss/pkg-plist	2006-03-31 06:43:20.000000000 -0300
+++ emboss/pkg-plist	2008-04-05 10:18:24.000000000 -0300
@@ -6,6 +6,7 @@
 bin/acdtrace
 bin/acdvalid
 bin/antigenic
+bin/backtranambig
 bin/backtranseq
 bin/banana
 bin/biosed
@@ -43,6 +44,7 @@
 bin/dotpath
 bin/dottup
 bin/dreg
+bin/edialign
 bin/einverted
 bin/embossdata
 bin/embossversion
@@ -54,6 +56,7 @@
 bin/equicktandem
 bin/est2genome
 bin/etandem
+bin/extractalign
 bin/extractfeat
 bin/extractseq
 bin/findkm
@@ -73,6 +76,8 @@
 bin/jembossctl
 bin/lindna
 bin/listor
+bin/makenucseq
+bin/makeprotseq
 bin/marscan
 bin/maskfeat
 bin/maskseq
@@ -138,11 +143,11 @@
 bin/sirna
 bin/sixpack
 bin/skipseq
-bin/syco
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
+bin/syco
 bin/tcode
 bin/textsearch
 bin/tfextract
@@ -160,22 +165,29 @@
 bin/whichdb
 bin/wobble
 bin/wordcount
+bin/wordfinder
 bin/wordmatch
 bin/wossname
 bin/yank
 bin/runJemboss.csh
-include/drivers.h
-include/pdf.h
-include/plcore.h
-include/plevent.h
-include/plplotP.h
-include/plxwd.h
-include/metadefs.h
-include/plConfig.h
-include/pldebug.h
-include/plplot.h
-include/plstrm.h
-include/plDevs.h
+include/eplplot/drivers.h
+include/eplplot/pdf.h
+include/eplplot/plcore.h
+include/eplplot/plevent.h
+include/eplplot/plplotP.h
+include/eplplot/plxwd.h
+include/eplplot/metadefs.h
+include/eplplot/plConfig.h
+include/eplplot/pldebug.h
+include/eplplot/plplot.h
+include/eplplot/plstrm.h
+include/eplplot/plDevs.h
+include/eplplot/disptab.h
+include/eplplot/pldll.h
+include/eplplot/plhershey-unicode.h
+include/eplplot/ps.h
+include/eplplot/plunicode-type1.h
+include/eplplot/plfci-type1.h
 include/ajax.h
 include/ajarch.h
 include/ajdefine.h
@@ -188,6 +200,7 @@
 include/ajcod.h
 include/ajdan.h
 include/ajdmx.h
+include/ajdom.h
 include/ajdomain.h
 include/ajexcept.h
 include/ajfeat.h
@@ -207,6 +220,7 @@
 include/ajmess.h
 include/ajnam.h
 include/ajnexus.h
+include/ajpat.h
 include/ajpdb.h
 include/ajpdbio.h
 include/ajphylo.h
@@ -255,716 +269,29 @@
 include/embmol.h
 include/embnmer.h
 include/embpat.h
+include/embpatlist.h
 include/embprop.h
 include/embpdb.h
 include/embread.h
 include/embsig.h
 include/embshow.h
 include/embword.h
-lib/libplplot.so.5
-lib/libplplot.so
-lib/libplplot.la
-lib/libplplot.a
-lib/libajax.so.3
+lib/libeplplot.so.5
+lib/libeplplot.so
+lib/libeplplot.la
+lib/libeplplot.a
+lib/libajax.so.5
 lib/libajax.so
 lib/libajax.la
 lib/libajax.a
-lib/libajaxg.so.3
+lib/libajaxg.so.5
 lib/libajaxg.so
 lib/libajaxg.la
 lib/libajaxg.a
-lib/libnucleus.so.3
+lib/libnucleus.so.5
 lib/libnucleus.so
 lib/libnucleus.la
 lib/libnucleus.a
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
-%%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.toc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.1.syco.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.1.tmap.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.1.wobble.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/aaindexextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acd_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdlog.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdpretty.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdtable.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdtrace.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdvalid.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ajtest.html
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+%%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%%/tutorials/emboss-gcg.ppt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt
+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/DragTree.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html
 %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html
@@ -1913,6 +1689,7 @@
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiTextField.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
 %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
@@ -2006,28 +1783,31 @@
 %%DATADIR%%/jemboss/readme.html
 %%DATADIR%%/jemboss/runJemboss.sh
 %%DATADIR%%/jemboss/README
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm include/eplplot
+@dirrm include
 @dirrm %%DATADIR%%/acd
-@dirrm %%DATADIR%%/data/AAINDEX
-@dirrm %%DATADIR%%/data/CODONS
-@dirrm %%DATADIR%%/data/REBASE
-@dirrm %%DATADIR%%/data/PRINTS
-@dirrm %%DATADIR%%/data/PROSITE
+@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/gb
 @dirrm %%DATADIR%%/test/pir
 @dirrm %%DATADIR%%/test/swiss
 @dirrm %%DATADIR%%/test/swnew
-@dirrm %%DATADIR%%/test/wormpep
+@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%%/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
@@ -2067,5 +1847,4 @@
 @dirrmtry bin
 @dirrmtry include
 @dirrmtry lib
-@dirrmtry share/doc
 @dirrmtry share
