4 files changed, 385 insertions, 387 deletions
diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
index 9726a4b282f1..dd13799ea239 100644
--- a/biology/p5-AcePerl/Makefile
+++ b/biology/p5-AcePerl/Makefile
@@ -15,7 +15,7 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	philip@p6m7g8.com
 COMMENT=	Perl5 interface to the ACEDB genome database system
 
-BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Digest/MD5.pm:${PORTSDIR}/security/p5-Digest-MD5
+BUILD_DEPENDS=	${SITE_PERL}/${PERL_ARCH}/Digest/MD5.pm:${PORTSDIR}/security/p5-Digest-MD5
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 PERL_CONFIGURE=	yes
@@ -39,7 +39,6 @@ MAN3=		Ace.3 Ace::Browser::AceSubs.3 Ace::Browser::SearchSubs.3 \
 		Ace::Sequence::GappedAlignment.3 Ace::Sequence::Gene.3 \
 		Ace::Sequence::Homol.3 Ace::Sequence::Multi.3 \
 		Ace::Sequence::Transcript.3
-MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
 
 post-patch:
 	@ ${SED} -e 's|XX__CC__XX|${CC}|' < ${FILESDIR}/FREEBSD_DEF \
diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist
index acf0566bc863..e37eb6b70a06 100644
--- a/biology/p5-AcePerl/pkg-plist
+++ b/biology/p5-AcePerl/pkg-plist
@@ -1,121 +1,121 @@
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Browser/AceSubs.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Browser/GeneSubs.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Browser/SearchSubs.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Browser/SiteDefs.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Browser/TreeSubs.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Freesubs.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Fk.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/anchored_arrow.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/arrow.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/box.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/crossbox.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/dot.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/ex.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/graded_segments.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/group.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/line.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/primers.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/segments.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/span.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/toomany.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/transcript.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/triangle.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/GlyphFactory.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Panel.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Track.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Local.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Model.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object/Wormbase.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/RPC.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/GappedAlignment.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Gene.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Transcript.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/SocketServer.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/AceSubs.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/GeneSubs.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/SearchSubs.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/SiteDefs.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/TreeSubs.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Freesubs.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Fk.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/anchored_arrow.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/arrow.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/box.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/crossbox.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/dot.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/ex.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/graded_segments.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/group.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/line.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/primers.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/segments.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/span.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/toomany.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/transcript.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/triangle.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/GlyphFactory.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Panel.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Track.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Iterator.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Local.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Model.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object/Wormbase.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/RPC.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/GappedAlignment.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Gene.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Transcript.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/Ace/SocketServer.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/GFF/Filehandle.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.bs
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.so
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asXML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asXML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/escapeXML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.bs
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.so
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_restore_iterator.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_save_iterator.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/datetime.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/find.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/freeprotect.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/ping.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/split.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/timestamps.al
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/RPC
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics/Glyph
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Graphics
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Browser
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/.packlist
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.bs
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.so
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asXML.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asXML.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/escapeXML.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.bs
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.so
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_restore_iterator.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_save_iterator.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/class_count.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/classes.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/count.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/date.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/date_style.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/datetime.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/find.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/freeprotect.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/grep.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/layout.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/new.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/pick.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/ping.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/put.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/split.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/status.al
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/timestamps.al
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/GFF
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 28ae5758aaf0..af0afeccb335 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -20,16 +20,16 @@ COMMENT=	A collection of Perl modules for bioinformatics
 
 # These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
 # prevents a flood of build-time warnings.
-BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
-		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
+BUILD_DEPENDS=	${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
+		${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
+		${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
+		${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
+		${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
+		${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
+		${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
+		${SITE_PERL}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
+		${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
+		${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 PERL_CONFIGURE=	YES
@@ -47,12 +47,12 @@ DISTFILES+=	bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX}
 EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
 
 .if defined(WITH_CORBA_CLIENT)
-BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
-RUN_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+BUILD_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+RUN_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
 .endif
 .if defined(WITH_CORBA_SERVER)
-BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
-RUN_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+BUILD_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+RUN_DEPENDS+=	${SITE_PERL}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
 .endif
 .if defined(WITH_GUI)
 RUN_DEPENDS+=	ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
@@ -171,7 +171,6 @@ MAN3+=		Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \
 .if defined(WITH_GUI)
 MAN3+=		Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3
 .endif
-MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
 
 pre-fetch:
 .if !defined(BATCH) && (!defined(WITH_CORBA_CLIENT) || \
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index ad038a26dacf..29c40be66b26 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1,250 +1,250 @@
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Base.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Client.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/ORB.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/PrimarySeq.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Seq.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/SeqFeature.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Biocorba.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/biocorba.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/AnonymousSeq.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Base.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/BioEnv.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeq.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqDB.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqIterator.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqVector.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Seq.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqDB.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeature.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeatureIterator.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeatureVector.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Server.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/AnnotMap.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/BioTkPerl8_1.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/GO_Browser.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/HitDisplay.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/README
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/SeqCanvas.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/Tkpsh.pl
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Map.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_SeqSubs.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Sequence.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Utilities.pm
-%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Tk/.packlist
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/bl2seq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/clustalw.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/mase.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/msf.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/pfam.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/prodom.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/selex.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/AlignIO/stockholm.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GDB.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/NCBIHelper.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SwissProt.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/UpdateableSeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/WebDBSeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/DBLinkContainerI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/DriverFactory.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactory.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Factory/SeqAnalysisParserFactoryI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/GenBank.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Swissprot.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/AARange.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Chain.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/ChainI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/DNA.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Exon.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Gene.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/BioPerl.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/Loader.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/IO/SRS.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Intron.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutation.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Mutator.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Prim_Transcript.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Range.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Region.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Repeat_Unit.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/SeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Transcript.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LiveSeq/Translation.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/AvWithinCoordPolicy.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/CoordinatePolicyI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Fuzzy.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/FuzzyLocationI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/NarrowestCoordPolicy.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Simple.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/Split.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/SplitLocationI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Location/WidestCoordPolicy.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/LocationI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IO.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargePrimarySeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/LargeSeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq/RichSeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqAnalysisParserI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Exon.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/ExonI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructure.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/GeneStructureI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/Transcript.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Gene/TranscriptI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Similarity.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/SimilarityPair.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/ace.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/featureHandler.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/idHandler.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/game/seqHandler.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/largefasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqUtils.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AnalysisResult.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPbl2seq.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/HSP.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Iteration.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPlite/Sbjct.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/BPpsilite.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/ESTScan.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/GFF.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Genscan.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/MZEF.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/OddCodes.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Exon.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Prediction/Gene.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/Clustalw.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/Alignment/TCoffee.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Run/StandAloneBlast.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAChange.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/AAReverseMutate.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/Allele.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/DNAMutation.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/flat.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO/xml.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/README
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/RNAChange.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/SeqDiff.pm
-lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/VariantI.pm
-lib/perl5/site_perl/%%PERL_VER%%/bioback.pod
-lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
-lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
-lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
-lib/perl5/site_perl/%%PERL_VER%%/bptutorial.pl
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