- Update to 1.007001

- Update *_DEPENDS
- Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies
- Use PORTDATA, PORTDOCS and PORTEXAMPLES

Changes:	http://search.cpan.org/dist/BioPerl/Changes

6 files changed, 180 insertions, 383 deletions

diff --git a/biology/p5-BioPerl/Makefile b/biology/p5-BioPerl/Makefile
index b4d1bc17a645..7fe6fe0f6b00 100644
--- a/biology/p5-BioPerl/Makefile
+++ b/biology/p5-BioPerl/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl
-PORTVERSION=	1.6.924
-PORTREVISION=	5
+PORTVERSION=	1.007001
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
@@ -17,50 +16,52 @@ LICENSE_COMB=	dual
 
 BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
 		p5-Array-Compare>=0:misc/p5-Array-Compare \
-		p5-Class-AutoClass>=0:devel/p5-Class-AutoClass \
 		p5-Clone>=0:devel/p5-Clone \
 		p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \
 		p5-DBD-mysql>=0:databases/p5-DBD-mysql \
-		p5-Data-Stag>=0:devel/p5-Data-Stag \
+		p5-DBI>=0:databases/p5-DBI \
+		p5-Data-Stag>=0.11:devel/p5-Data-Stag \
 		p5-Error>=0:lang/p5-Error \
 		p5-GD>=0:graphics/p5-GD \
-		p5-GD-SVG>=0:graphics/p5-GD-SVG \
-		p5-Graph>=0:math/p5-Graph \
+		p5-Graph>=0.50:math/p5-Graph \
 		p5-GraphViz>=0:graphics/p5-GraphViz \
-		p5-HTML-Parser>=0:www/p5-HTML-Parser \
-		p5-HTML-TableExtract>=2:www/p5-HTML-TableExtract \
+		p5-HTML-Parser>=3:www/p5-HTML-Parser \
+		p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \
+		p5-HTTP-Message>=0:www/p5-HTTP-Message \
 		p5-IO-String>=0:devel/p5-IO-String \
 		p5-IO-stringy>=0:devel/p5-IO-stringy \
-		p5-Math-Random>=0:math/p5-Math-Random \
+		p5-Inline-C>=0.67:devel/p5-Inline-C \
+		p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
 		p5-PostScript>=0:print/p5-PostScript \
-		p5-SOAP-Lite>=0:net/p5-SOAP-Lite \
-		p5-SVG>=0:textproc/p5-SVG \
-		p5-SVG-Graph>=0:graphics/p5-SVG-Graph \
+		p5-SVG>=2.26:textproc/p5-SVG \
+		p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \
 		p5-Set-Scalar>=0:devel/p5-Set-Scalar \
-		p5-Sort-Naturally>=1:textproc/p5-Sort-Naturally \
+		p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \
 		p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \
-		p5-Test-Most>=0:devel/p5-Test-Most \
-		p5-Text-Shellwords>=0:textproc/p5-Text-Shellwords \
-		p5-Text-Tabs+Wrap>=0:textproc/p5-Text-Tabs+Wrap \
-		p5-URI>=0:net/p5-URI \
 		p5-XML-DOM>=0:textproc/p5-XML-DOM \
 		p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \
 		p5-XML-LibXML>=0:textproc/p5-XML-LibXML \
 		p5-XML-Parser>=0:textproc/p5-XML-Parser \
-		p5-XML-SAX>=0:textproc/p5-XML-SAX \
+		p5-XML-SAX>=0.15:textproc/p5-XML-SAX \
 		p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \
-		p5-XML-Simple>=2:textproc/p5-XML-Simple \
+		p5-XML-Simple>=0:textproc/p5-XML-Simple \
 		p5-XML-Twig>=0:textproc/p5-XML-Twig \
-		p5-XML-Writer>=0:textproc/p5-XML-Writer \
+		p5-XML-Writer>=0.400:textproc/p5-XML-Writer \
 		p5-YAML>=0:textproc/p5-YAML \
 		p5-libwww>=0:www/p5-libwww \
 		p5-libxml>=0:textproc/p5-libxml
 RUN_DEPENDS:=	${BUILD_DEPENDS}
+TEST_DEPENDS=	p5-Test-Most>=0:devel/p5-Test-Most \
+		p5-URI>=0:net/p5-URI
 
 USES=		perl5
 USE_PERL5=	modbuild
 NO_ARCH=	yes
 
+PORTDATA=	*
+PORTDOCS=	*
+PORTEXAMPLES=	*
+
 OPTIONS_DEFINE=	DOCS EXAMPLES PGTEST SQLITETEST
 PGTEST_DESC=	Test PostGreSQL
 SQLITETEST_DESC=	Test SQLite
@@ -70,7 +71,7 @@ SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
 SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
 
 post-patch:
-	@${FIND} ${WRKSRC}/examples ${WRKSRC}/doc -name "*.pl" -o -name "*.cgi" \
+	@${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \
 		-o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \
 		'1s|(/usr)?/bin/perl|${PERL}|'
 
@@ -80,13 +81,20 @@ post-install:
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
-	${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
+.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md
+	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
 .endfor
-	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}
+	${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR}
 
 post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
 
-.include <bsd.port.mk>
+.include <bsd.port.pre.mk>
+
+.if ${PERL_LEVEL} >= 502200
+BUILD_DEPENDS+=	p5-CGI>=0:www/p5-CGI
+RUN_DEPENDS+=	p5-CGI>=0:www/p5-CGI
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/p5-BioPerl/distinfo b/biology/p5-BioPerl/distinfo
index f8ce60817098..de8de98486f3 100644
--- a/biology/p5-BioPerl/distinfo
+++ b/biology/p5-BioPerl/distinfo
@@ -1,2 +1,3 @@
-SHA256 (BioPerl-1.6.924.tar.gz) = 616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0
-SIZE (BioPerl-1.6.924.tar.gz) = 12623118
+TIMESTAMP = 1479828383
+SHA256 (BioPerl-1.007001.tar.gz) = 9da1dbcd10452f53194c98c6cc2f604a59124507dcc1e6a8440565f44dd07b40
+SIZE (BioPerl-1.007001.tar.gz) = 12486953
diff --git a/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm b/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
index b4433616c5fc..09e7054f034a 100644
--- a/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
+++ b/biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
@@ -1,5 +1,5 @@
---- Bio/Root/Build.pm.orig	2014-07-10 22:13:23.000000000 +0200
-+++ Bio/Root/Build.pm	2014-07-24 11:55:59.000000000 +0200
+--- Bio/Root/Build.pm.orig	2014-07-10 20:13:23 UTC
++++ Bio/Root/Build.pm
 @@ -83,49 +83,9 @@
          }
      }
diff --git a/biology/p5-BioPerl/files/patch-Build.PL b/biology/p5-BioPerl/files/patch-Build.PL
index 4f890bf60809..d86c52a42105 100644
--- a/biology/p5-BioPerl/files/patch-Build.PL
+++ b/biology/p5-BioPerl/files/patch-Build.PL
@@ -1,70 +1,79 @@
---- Build.PL.orig	2009-09-30 00:33:45.000000000 +0800
-+++ Build.PL	2009-12-01 10:25:51.000000000 +0800
-@@ -187,7 +187,6 @@
-                            },
+--- Build.PL.orig	2016-11-06 03:59:41 UTC
++++ Build.PL
+@@ -226,7 +226,6 @@ my $build = Bio::Root::Build->new(
  
-     build_requires      => {
--                            'CPAN'                      => 1.81,
-                             'Module::Build'             => 0.2805,
-                             'Test::Harness'             => 2.62,
-                             'Test::Most'                => 0,
-@@ -376,86 +375,8 @@
+     build_requires => {
+         'Module::Build' => 0.42,
+-        'CPAN'          => 1.81,
+         'Test::Harness' => 2.62,
+         'Test::Most'    => 0,
+         'URI::Escape'   => 0
+@@ -413,101 +412,8 @@ sub test_biodbgff {
  
  sub prompt_for_biodb {
      my $accept = shift;
--    my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
--                              "Bio::DB::SeqFeature::Store live database tests? ".
--                              "y/n", 'n');
+-    my $proceed = $accept ? 0 : $build->y_n(
+-        "Do you want to run the Bio::DB::GFF or "
+-            . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
+-        'n'
+-    );
 -
 -    if ($proceed) {
 -        my @driver_choices;
--        foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
--            if (grep {/$poss/i} @drivers) {
+-        foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
+-            if ( grep {/$poss/i} @drivers ) {
 -                my $choice = $poss;
 -                $choice =~ s/^(.)/[$1]/;
--                push(@driver_choices, $choice);
+-                push( @driver_choices, $choice );
 -            }
 -        }
 -
 -        my $driver;
--        if (@driver_choices > 1) {
+-        if ( @driver_choices > 1 ) {
 -            my ($default) = $driver_choices[0] =~ /\[(.)/;
--            $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
--        }
--        else {
+-            $driver = $build->prompt(
+-                "Which database driver should be used? "
+-                    . join( " ", @driver_choices ),
+-                $default
+-            );
+-        } else {
 -            ($driver) = $driver_choices[0] =~ /\[(.)/;
 -        }
--        if ($driver =~ /^[mM]/) {
+-        if ( $driver =~ /^[mM]/ ) {
 -            $driver = 'mysql';
--        }
--        elsif ($driver =~ /^[pP]/) {
+-        } elsif ( $driver =~ /^[pP]/ ) {
 -            $driver = 'Pg';
--        }
--        elsif ($driver =~ /^[oO]/) {
+-        } elsif ( $driver =~ /^[oO]/ ) {
 -            $driver = 'Oracle';
--        }
--        elsif ($driver =~ /^[sS]/) {
+-        } elsif ( $driver =~ /^[sS]/ ) {
 -            $driver = 'SQLite';
 -        }
 -
--        my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
--                                     "This database should already be present but doesn't have to ".
--                                     "be preloaded for any schema", 'test');
--        my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
--        my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
--        my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
+-        my $test_db = $build->prompt(
+-            "Which database should I use for testing the $driver driver?\n"
+-                . "This database should already be present but doesn't have to "
+-                . "be preloaded for any schema",
+-            'test'
+-        );
+-        my $test_host = $build->prompt(
+-            "On which host is database '$test_db' running (hostname, ip address or host:port)",
+-            'localhost'
+-        );
+-        my $test_user = $build->prompt(
+-            "User name for connecting to database '$test_db'?", 'undef' );
+-        my $test_pass = $build->prompt(
+-            "Password for connecting to database '$test_db'?", 'undef' );
 -
 -        my $use_host = 1;
--        if ($test_host eq 'undef' || $test_host eq 'localhost') {
+-        if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
 -            $use_host = 0;
 -        }
 -
 -        my $test_dsn;
--        if ($driver eq 'Pg' || $driver eq 'SQLite') {
+-        if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
 -            $test_dsn = "dbi:$driver:dbname=$test_db";
 -            $mysql_ok = 0;
--        }
--        else {
+-        } else {
 -            $test_dsn = "dbi:$driver:database=$test_db";
 -            $mysql_ok = 0;
 -        }
@@ -72,24 +81,30 @@
 -            $test_dsn .= ";host=$test_host";
 -        }
 -
--        $build->notes(dbd_driver => $driver);
--        $build->notes(test_db => $test_db);
--        $build->notes(test_host => $test_host);
--        $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
--        $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
--        $build->notes(test_dsn => $test_dsn);
+-        $build->notes( dbd_driver => $driver );
+-        $build->notes( test_db    => $test_db );
+-        $build->notes( test_host  => $test_host );
+-        $build->notes(
+-            test_user => $test_user eq 'undef' ? undef : $test_user );
+-        $build->notes(
+-            test_pass => $test_pass eq 'undef' ? undef : $test_pass );
+-        $build->notes( test_dsn => $test_dsn );
 -
--        $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
--                        "    Database $test_db\n",
--                        "    Host     $test_host\n",
--                        "    DSN      $test_dsn\n",
--                        "    User     $test_user\n",
--                        "    Password $test_pass\n");
--        $build->log_info("  - will not run the BioDBSeqFeature live ".
--                         "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
--    }
--    else {
--        $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
+-        $build->log_info(
+-            "  - will run tests with database driver '$driver' and these settings:\n",
+-            "    Database $test_db\n",
+-            "    Host     $test_host\n",
+-            "    DSN      $test_dsn\n",
+-            "    User     $test_user\n",
+-            "    Password $test_pass\n"
+-        );
+-        $build->log_info( "  - will not run the BioDBSeqFeature live "
+-                . "database tests (requires MySQL or Pg driver)\n" )
+-            unless ( $driver eq 'mysql' or $driver eq 'Pg' );
+-    } else {
+-        $build->log_info(
+-            "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
+-        );
 -    }
 -
 +    my $proceed = 0;
diff --git a/biology/p5-BioPerl/pkg-descr b/biology/p5-BioPerl/pkg-descr
index a993ffada2fe..93e2a521ae67 100644
--- a/biology/p5-BioPerl/pkg-descr
+++ b/biology/p5-BioPerl/pkg-descr
@@ -1,8 +1,8 @@
-The Bioperl Project is an international association of developers of open
+The BioPerl Project is an international association of developers of open
 source Perl tools for bioinformatics, genomics and life science research.
 
-Bioperl is a collection of object-oriented Perl modules created by the
-Bioperl Project.  It forms the basis of a large number of bioinformatics and
+BioPerl is a collection of object-oriented Perl modules created by the
+BioPerl Project. It forms the basis of a large number of bioinformatics and
 genomics applications.
 
 (For an interesting aside on "How Perl saved the Human Genome Project", see
diff --git a/biology/p5-BioPerl/pkg-plist b/biology/p5-BioPerl/pkg-plist
index 4f532432a681..f24234684afb 100644
--- a/biology/p5-BioPerl/pkg-plist
+++ b/biology/p5-BioPerl/pkg-plist
@@ -15,6 +15,7 @@ bin/bp_fast_load_gff.pl
 bin/bp_fastam9_to_table.pl
 bin/bp_fetch.pl
 bin/bp_filter_search.pl
+bin/bp_find-blast-matches.pl
 bin/bp_flanks.pl
 bin/bp_gccalc.pl
 bin/bp_genbank2gff.pl
@@ -43,7 +44,6 @@ bin/bp_process_wormbase.pl
 bin/bp_query_entrez_taxa.pl
 bin/bp_remote_blast.pl
 bin/bp_revtrans-motif.pl
-bin/bp_search2BSML.pl
 bin/bp_search2alnblocks.pl
 bin/bp_search2gff.pl
 bin/bp_search2table.pl
@@ -139,18 +139,6 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/ClusterIO/unigene.pm
 %%SITE_PERL%%/Bio/CodonUsage/IO.pm
 %%SITE_PERL%%/Bio/CodonUsage/Table.pm
-%%SITE_PERL%%/Bio/Coordinate/Chain.pm
-%%SITE_PERL%%/Bio/Coordinate/Collection.pm
-%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm
-%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
-%%SITE_PERL%%/Bio/Coordinate/Graph.pm
-%%SITE_PERL%%/Bio/Coordinate/MapperI.pm
-%%SITE_PERL%%/Bio/Coordinate/Pair.pm
-%%SITE_PERL%%/Bio/Coordinate/Result.pm
-%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm
-%%SITE_PERL%%/Bio/Coordinate/Result/Match.pm
-%%SITE_PERL%%/Bio/Coordinate/ResultI.pm
-%%SITE_PERL%%/Bio/Coordinate/Utils.pm
 %%SITE_PERL%%/Bio/DB/Ace.pm
 %%SITE_PERL%%/Bio/DB/BioFetch.pm
 %%SITE_PERL%%/Bio/DB/CUTG.pm
@@ -257,7 +245,6 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/DB/SeqFeature/Store/berkeleydb.pm
 %%SITE_PERL%%/Bio/DB/SeqFeature/Store/berkeleydb3.pm
 %%SITE_PERL%%/Bio/DB/SeqFeature/Store/memory.pm
-%%SITE_PERL%%/Bio/DB/SeqHound.pm
 %%SITE_PERL%%/Bio/DB/SeqI.pm
 %%SITE_PERL%%/Bio/DB/SeqVersion.pm
 %%SITE_PERL%%/Bio/DB/SeqVersion/gi.pm
@@ -270,6 +257,7 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/DB/Taxonomy/greengenes.pm
 %%SITE_PERL%%/Bio/DB/Taxonomy/list.pm
 %%SITE_PERL%%/Bio/DB/Taxonomy/silva.pm
+%%SITE_PERL%%/Bio/DB/Taxonomy/sqlite.pm
 %%SITE_PERL%%/Bio/DB/Universal.pm
 %%SITE_PERL%%/Bio/DB/UpdateableSeqI.pm
 %%SITE_PERL%%/Bio/DB/WebDBSeqI.pm
@@ -502,6 +490,7 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Root/RootI.pm
 %%SITE_PERL%%/Bio/Root/Storable.pm
 %%SITE_PERL%%/Bio/Root/Test.pm
+%%SITE_PERL%%/Bio/Root/TestObject.pm
 %%SITE_PERL%%/Bio/Root/Utilities.pm
 %%SITE_PERL%%/Bio/Root/Version.pm
 %%SITE_PERL%%/Bio/Search/BlastStatistics.pm
@@ -543,6 +532,7 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Search/Result/GenericResult.pm
 %%SITE_PERL%%/Bio/Search/Result/HMMERResult.pm
 %%SITE_PERL%%/Bio/Search/Result/HmmpfamResult.pm
+%%SITE_PERL%%/Bio/Search/Result/INFERNALResult.pm
 %%SITE_PERL%%/Bio/Search/Result/PullResultI.pm
 %%SITE_PERL%%/Bio/Search/Result/ResultFactory.pm
 %%SITE_PERL%%/Bio/Search/Result/ResultI.pm
@@ -560,20 +550,16 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
 %%SITE_PERL%%/Bio/SearchIO/SearchResultEventBuilder.pm
 %%SITE_PERL%%/Bio/SearchIO/SearchWriterI.pm
-%%SITE_PERL%%/Bio/SearchIO/Writer/BSMLResultWriter.pm
 %%SITE_PERL%%/Bio/SearchIO/Writer/GbrowseGFF.pm
 %%SITE_PERL%%/Bio/SearchIO/Writer/HSPTableWriter.pm
 %%SITE_PERL%%/Bio/SearchIO/Writer/HTMLResultWriter.pm
 %%SITE_PERL%%/Bio/SearchIO/Writer/HitTableWriter.pm
 %%SITE_PERL%%/Bio/SearchIO/Writer/ResultTableWriter.pm
 %%SITE_PERL%%/Bio/SearchIO/Writer/TextResultWriter.pm
-%%SITE_PERL%%/Bio/SearchIO/XML/BlastHandler.pm
-%%SITE_PERL%%/Bio/SearchIO/XML/PsiBlastHandler.pm
 %%SITE_PERL%%/Bio/SearchIO/axt.pm
 %%SITE_PERL%%/Bio/SearchIO/blast.pm
 %%SITE_PERL%%/Bio/SearchIO/blast_pull.pm
 %%SITE_PERL%%/Bio/SearchIO/blasttable.pm
-%%SITE_PERL%%/Bio/SearchIO/blastxml.pm
 %%SITE_PERL%%/Bio/SearchIO/cross_match.pm
 %%SITE_PERL%%/Bio/SearchIO/erpin.pm
 %%SITE_PERL%%/Bio/SearchIO/exonerate.pm
@@ -744,7 +730,6 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Tools/Analysis/Protein/ELM.pm
 %%SITE_PERL%%/Bio/Tools/Analysis/Protein/GOR4.pm
 %%SITE_PERL%%/Bio/Tools/Analysis/Protein/HNN.pm
-%%SITE_PERL%%/Bio/Tools/Analysis/Protein/Mitoprot.pm
 %%SITE_PERL%%/Bio/Tools/Analysis/Protein/NetPhos.pm
 %%SITE_PERL%%/Bio/Tools/Analysis/Protein/Scansite.pm
 %%SITE_PERL%%/Bio/Tools/Analysis/Protein/Sopma.pm
@@ -756,7 +741,6 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Tools/ECnumber.pm
 %%SITE_PERL%%/Bio/Tools/EMBOSS/Palindrome.pm
 %%SITE_PERL%%/Bio/Tools/EPCR.pm
-%%SITE_PERL%%/Bio/Tools/ERPIN.pm
 %%SITE_PERL%%/Bio/Tools/ESTScan.pm
 %%SITE_PERL%%/Bio/Tools/Eponine.pm
 %%SITE_PERL%%/Bio/Tools/Est2Genome.pm
@@ -777,7 +761,6 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Tools/HMMER/Set.pm
 %%SITE_PERL%%/Bio/Tools/Hmmpfam.pm
 %%SITE_PERL%%/Bio/Tools/IUPAC.pm
-%%SITE_PERL%%/Bio/Tools/Infernal.pm
 %%SITE_PERL%%/Bio/Tools/Lucy.pm
 %%SITE_PERL%%/Bio/Tools/MZEF.pm
 %%SITE_PERL%%/Bio/Tools/Match.pm
@@ -805,18 +788,11 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Tools/Protparam.pm
 %%SITE_PERL%%/Bio/Tools/Pseudowise.pm
 %%SITE_PERL%%/Bio/Tools/QRNA.pm
-%%SITE_PERL%%/Bio/Tools/RNAMotif.pm
 %%SITE_PERL%%/Bio/Tools/RandomDistFunctions.pm
 %%SITE_PERL%%/Bio/Tools/RepeatMasker.pm
 %%SITE_PERL%%/Bio/Tools/Run/GenericParameters.pm
 %%SITE_PERL%%/Bio/Tools/Run/ParametersI.pm
 %%SITE_PERL%%/Bio/Tools/Run/RemoteBlast.pm
-%%SITE_PERL%%/Bio/Tools/Run/StandAloneBlast.pm
-%%SITE_PERL%%/Bio/Tools/Run/StandAloneNCBIBlast.pm
-%%SITE_PERL%%/Bio/Tools/Run/StandAloneWUBlast.pm
-%%SITE_PERL%%/Bio/Tools/Run/WrapperBase.pm
-%%SITE_PERL%%/Bio/Tools/Run/WrapperBase/CommandExts.pm
-%%SITE_PERL%%/Bio/Tools/Run/hmmer3.pm
 %%SITE_PERL%%/Bio/Tools/Seg.pm
 %%SITE_PERL%%/Bio/Tools/SeqPattern.pm
 %%SITE_PERL%%/Bio/Tools/SeqPattern/Backtranslate.pm
@@ -880,6 +856,69 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Variation/SeqDiff.pm
 %%SITE_PERL%%/Bio/Variation/VariantI.pm
 %%SITE_PERL%%/Bio/WebAgent.pm
+%%PERL5_MAN1%%/bp_aacomp.pl.1.gz
+%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.pl.1.gz
+%%PERL5_MAN1%%/bp_bioflat_index.pl.1.gz
+%%PERL5_MAN1%%/bp_biogetseq.pl.1.gz
+%%PERL5_MAN1%%/bp_blast2tree.pl.1.gz
+%%PERL5_MAN1%%/bp_bulk_load_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_chaos_plot.pl.1.gz
+%%PERL5_MAN1%%/bp_classify_hits_kingdom.pl.1.gz
+%%PERL5_MAN1%%/bp_composite_LD.pl.1.gz
+%%PERL5_MAN1%%/bp_dbsplit.pl.1.gz
+%%PERL5_MAN1%%/bp_download_query_genbank.pl.1.gz
+%%PERL5_MAN1%%/bp_extract_feature_seq.pl.1.gz
+%%PERL5_MAN1%%/bp_fast_load_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_fastam9_to_table.pl.1.gz
+%%PERL5_MAN1%%/bp_fetch.pl.1.gz
+%%PERL5_MAN1%%/bp_filter_search.pl.1.gz
+%%PERL5_MAN1%%/bp_find-blast-matches.pl.1.gz
+%%PERL5_MAN1%%/bp_flanks.pl.1.gz
+%%PERL5_MAN1%%/bp_gccalc.pl.1.gz
+%%PERL5_MAN1%%/bp_genbank2gff.pl.1.gz
+%%PERL5_MAN1%%/bp_genbank2gff3.pl.1.gz
+%%PERL5_MAN1%%/bp_generate_histogram.pl.1.gz
+%%PERL5_MAN1%%/bp_heterogeneity_test.pl.1.gz
+%%PERL5_MAN1%%/bp_hivq.pl.1.gz
+%%PERL5_MAN1%%/bp_hmmer_to_table.pl.1.gz
+%%PERL5_MAN1%%/bp_index.pl.1.gz
+%%PERL5_MAN1%%/bp_load_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_local_taxonomydb_query.pl.1.gz
+%%PERL5_MAN1%%/bp_make_mrna_protein.pl.1.gz
+%%PERL5_MAN1%%/bp_mask_by_search.pl.1.gz
+%%PERL5_MAN1%%/bp_meta_gff.pl.1.gz
+%%PERL5_MAN1%%/bp_mrtrans.pl.1.gz
+%%PERL5_MAN1%%/bp_mutate.pl.1.gz
+%%PERL5_MAN1%%/bp_netinstall.pl.1.gz
+%%PERL5_MAN1%%/bp_nexus2nh.pl.1.gz
+%%PERL5_MAN1%%/bp_nrdb.pl.1.gz
+%%PERL5_MAN1%%/bp_oligo_count.pl.1.gz
+%%PERL5_MAN1%%/bp_pairwise_kaks.pl.1.gz
+%%PERL5_MAN1%%/bp_parse_hmmsearch.pl.1.gz
+%%PERL5_MAN1%%/bp_process_gadfly.pl.1.gz
+%%PERL5_MAN1%%/bp_process_sgd.pl.1.gz
+%%PERL5_MAN1%%/bp_process_wormbase.pl.1.gz
+%%PERL5_MAN1%%/bp_query_entrez_taxa.pl.1.gz
+%%PERL5_MAN1%%/bp_remote_blast.pl.1.gz
+%%PERL5_MAN1%%/bp_revtrans-motif.pl.1.gz
+%%PERL5_MAN1%%/bp_search2alnblocks.pl.1.gz
+%%PERL5_MAN1%%/bp_search2gff.pl.1.gz
+%%PERL5_MAN1%%/bp_search2table.pl.1.gz
+%%PERL5_MAN1%%/bp_search2tribe.pl.1.gz
+%%PERL5_MAN1%%/bp_seq_length.pl.1.gz
+%%PERL5_MAN1%%/bp_seqconvert.pl.1.gz
+%%PERL5_MAN1%%/bp_seqcut.pl.1.gz
+%%PERL5_MAN1%%/bp_seqfeature_load.pl.1.gz
+%%PERL5_MAN1%%/bp_seqpart.pl.1.gz
+%%PERL5_MAN1%%/bp_seqret.pl.1.gz
+%%PERL5_MAN1%%/bp_seqretsplit.pl.1.gz
+%%PERL5_MAN1%%/bp_split_seq.pl.1.gz
+%%PERL5_MAN1%%/bp_sreformat.pl.1.gz
+%%PERL5_MAN1%%/bp_taxid4species.pl.1.gz
+%%PERL5_MAN1%%/bp_taxonomy2tree.pl.1.gz
+%%PERL5_MAN1%%/bp_translate_seq.pl.1.gz
+%%PERL5_MAN1%%/bp_tree2pag.pl.1.gz
+%%PERL5_MAN1%%/bp_unflatten_seq.pl.1.gz
 %%PERL5_MAN3%%/Bio::Align::AlignI.3.gz
 %%PERL5_MAN3%%/Bio::Align::DNAStatistics.3.gz
 %%PERL5_MAN3%%/Bio::Align::Graphics.3.gz
@@ -955,18 +994,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::ClusterIO::unigene.3.gz
 %%PERL5_MAN3%%/Bio::CodonUsage::IO.3.gz
 %%PERL5_MAN3%%/Bio::CodonUsage::Table.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Chain.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Collection.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::ExtrapolatingPair.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::GeneMapper.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Graph.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::MapperI.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Pair.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Result.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Result::Gap.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Result::Match.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::ResultI.3.gz
-%%PERL5_MAN3%%/Bio::Coordinate::Utils.3.gz
 %%PERL5_MAN3%%/Bio::DB::Ace.3.gz
 %%PERL5_MAN3%%/Bio::DB::BioFetch.3.gz
 %%PERL5_MAN3%%/Bio::DB::CUTG.3.gz
@@ -1072,7 +1099,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::berkeleydb.3.gz
 %%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::berkeleydb3.3.gz
 %%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::memory.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqHound.3.gz
 %%PERL5_MAN3%%/Bio::DB::SeqI.3.gz
 %%PERL5_MAN3%%/Bio::DB::SeqVersion.3.gz
 %%PERL5_MAN3%%/Bio::DB::SeqVersion::gi.3.gz
@@ -1085,6 +1111,7 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::DB::Taxonomy::greengenes.3.gz
 %%PERL5_MAN3%%/Bio::DB::Taxonomy::list.3.gz
 %%PERL5_MAN3%%/Bio::DB::Taxonomy::silva.3.gz
+%%PERL5_MAN3%%/Bio::DB::Taxonomy::sqlite.3.gz
 %%PERL5_MAN3%%/Bio::DB::Universal.3.gz
 %%PERL5_MAN3%%/Bio::DB::UpdateableSeqI.3.gz
 %%PERL5_MAN3%%/Bio::DB::WebDBSeqI.3.gz
@@ -1317,6 +1344,7 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Root::RootI.3.gz
 %%PERL5_MAN3%%/Bio::Root::Storable.3.gz
 %%PERL5_MAN3%%/Bio::Root::Test.3.gz
+%%PERL5_MAN3%%/Bio::Root::TestObject.3.gz
 %%PERL5_MAN3%%/Bio::Root::Utilities.3.gz
 %%PERL5_MAN3%%/Bio::Root::Version.3.gz
 %%PERL5_MAN3%%/Bio::Search::BlastStatistics.3.gz
@@ -1358,6 +1386,7 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Search::Result::GenericResult.3.gz
 %%PERL5_MAN3%%/Bio::Search::Result::HMMERResult.3.gz
 %%PERL5_MAN3%%/Bio::Search::Result::HmmpfamResult.3.gz
+%%PERL5_MAN3%%/Bio::Search::Result::INFERNALResult.3.gz
 %%PERL5_MAN3%%/Bio::Search::Result::PullResultI.3.gz
 %%PERL5_MAN3%%/Bio::Search::Result::ResultFactory.3.gz
 %%PERL5_MAN3%%/Bio::Search::Result::ResultI.3.gz
@@ -1375,20 +1404,16 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::SearchIO::IteratedSearchResultEventBuilder.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::SearchResultEventBuilder.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::SearchWriterI.3.gz
-%%PERL5_MAN3%%/Bio::SearchIO::Writer::BSMLResultWriter.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::Writer::GbrowseGFF.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::Writer::HSPTableWriter.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::Writer::HTMLResultWriter.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::Writer::HitTableWriter.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::Writer::ResultTableWriter.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::Writer::TextResultWriter.3.gz
-%%PERL5_MAN3%%/Bio::SearchIO::XML::BlastHandler.3.gz
-%%PERL5_MAN3%%/Bio::SearchIO::XML::PsiBlastHandler.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::axt.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::blast.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::blast_pull.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::blasttable.3.gz
-%%PERL5_MAN3%%/Bio::SearchIO::blastxml.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::cross_match.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::erpin.3.gz
 %%PERL5_MAN3%%/Bio::SearchIO::exonerate.3.gz
@@ -1559,7 +1584,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::ELM.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::GOR4.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::HNN.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::Mitoprot.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::NetPhos.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::Scansite.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Analysis::Protein::Sopma.3.gz
@@ -1571,7 +1595,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Tools::ECnumber.3.gz
 %%PERL5_MAN3%%/Bio::Tools::EMBOSS::Palindrome.3.gz
 %%PERL5_MAN3%%/Bio::Tools::EPCR.3.gz
-%%PERL5_MAN3%%/Bio::Tools::ERPIN.3.gz
 %%PERL5_MAN3%%/Bio::Tools::ESTScan.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Eponine.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Est2Genome.3.gz
@@ -1592,7 +1615,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Tools::HMMER::Set.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Hmmpfam.3.gz
 %%PERL5_MAN3%%/Bio::Tools::IUPAC.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Infernal.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Lucy.3.gz
 %%PERL5_MAN3%%/Bio::Tools::MZEF.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Match.3.gz
@@ -1620,17 +1642,11 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Tools::Protparam.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Pseudowise.3.gz
 %%PERL5_MAN3%%/Bio::Tools::QRNA.3.gz
-%%PERL5_MAN3%%/Bio::Tools::RNAMotif.3.gz
 %%PERL5_MAN3%%/Bio::Tools::RandomDistFunctions.3.gz
 %%PERL5_MAN3%%/Bio::Tools::RepeatMasker.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::GenericParameters.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::ParametersI.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::RemoteBlast.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlast.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneNCBIBlast.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::StandAloneWUBlast.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase::CommandExts.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Seg.3.gz
 %%PERL5_MAN3%%/Bio::Tools::SeqPattern.3.gz
 %%PERL5_MAN3%%/Bio::Tools::SeqPattern::Backtranslate.3.gz
@@ -1694,246 +1710,3 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Variation::SeqDiff.3.gz
 %%PERL5_MAN3%%/Bio::Variation::VariantI.3.gz
 %%PERL5_MAN3%%/Bio::WebAgent.3.gz
-%%PERL5_MAN1%%/bp_aacomp.pl.1.gz
-%%PERL5_MAN1%%/bp_biofetch_genbank_proxy.pl.1.gz
-%%PERL5_MAN1%%/bp_bioflat_index.pl.1.gz
-%%PERL5_MAN1%%/bp_biogetseq.pl.1.gz
-%%PERL5_MAN1%%/bp_blast2tree.pl.1.gz
-%%PERL5_MAN1%%/bp_bulk_load_gff.pl.1.gz
-%%PERL5_MAN1%%/bp_chaos_plot.pl.1.gz
-%%PERL5_MAN1%%/bp_classify_hits_kingdom.pl.1.gz
-%%PERL5_MAN1%%/bp_composite_LD.pl.1.gz
-%%PERL5_MAN1%%/bp_dbsplit.pl.1.gz
-%%PERL5_MAN1%%/bp_download_query_genbank.pl.1.gz
-%%PERL5_MAN1%%/bp_extract_feature_seq.pl.1.gz
-%%PERL5_MAN1%%/bp_fast_load_gff.pl.1.gz
-%%PERL5_MAN1%%/bp_fastam9_to_table.pl.1.gz
-%%PERL5_MAN1%%/bp_fetch.pl.1.gz
-%%PERL5_MAN1%%/bp_filter_search.pl.1.gz
-%%PERL5_MAN1%%/bp_flanks.pl.1.gz
-%%PERL5_MAN1%%/bp_gccalc.pl.1.gz
-%%PERL5_MAN1%%/bp_genbank2gff.pl.1.gz
-%%PERL5_MAN1%%/bp_genbank2gff3.pl.1.gz
-%%PERL5_MAN1%%/bp_generate_histogram.pl.1.gz
-%%PERL5_MAN1%%/bp_heterogeneity_test.pl.1.gz
-%%PERL5_MAN1%%/bp_hivq.pl.1.gz
-%%PERL5_MAN1%%/bp_hmmer_to_table.pl.1.gz
-%%PERL5_MAN1%%/bp_index.pl.1.gz
-%%PERL5_MAN1%%/bp_load_gff.pl.1.gz
-%%PERL5_MAN1%%/bp_local_taxonomydb_query.pl.1.gz
-%%PERL5_MAN1%%/bp_make_mrna_protein.pl.1.gz
-%%PERL5_MAN1%%/bp_mask_by_search.pl.1.gz
-%%PERL5_MAN1%%/bp_meta_gff.pl.1.gz
-%%PERL5_MAN1%%/bp_mrtrans.pl.1.gz
-%%PERL5_MAN1%%/bp_mutate.pl.1.gz
-%%PERL5_MAN1%%/bp_netinstall.pl.1.gz
-%%PERL5_MAN1%%/bp_nexus2nh.pl.1.gz
-%%PERL5_MAN1%%/bp_nrdb.pl.1.gz
-%%PERL5_MAN1%%/bp_oligo_count.pl.1.gz
-%%PERL5_MAN1%%/bp_pairwise_kaks.pl.1.gz
-%%PERL5_MAN1%%/bp_parse_hmmsearch.pl.1.gz
-%%PERL5_MAN1%%/bp_process_gadfly.pl.1.gz
-%%PERL5_MAN1%%/bp_process_sgd.pl.1.gz
-%%PERL5_MAN1%%/bp_process_wormbase.pl.1.gz
-%%PERL5_MAN1%%/bp_query_entrez_taxa.pl.1.gz
-%%PERL5_MAN1%%/bp_remote_blast.pl.1.gz
-%%PERL5_MAN1%%/bp_revtrans-motif.pl.1.gz
-%%PERL5_MAN1%%/bp_search2BSML.pl.1.gz
-%%PERL5_MAN1%%/bp_search2alnblocks.pl.1.gz
-%%PERL5_MAN1%%/bp_search2gff.pl.1.gz
-%%PERL5_MAN1%%/bp_search2table.pl.1.gz
-%%PERL5_MAN1%%/bp_search2tribe.pl.1.gz
-%%PERL5_MAN1%%/bp_seq_length.pl.1.gz
-%%PERL5_MAN1%%/bp_seqconvert.pl.1.gz
-%%PERL5_MAN1%%/bp_seqcut.pl.1.gz
-%%PERL5_MAN1%%/bp_seqfeature_load.pl.1.gz
-%%PERL5_MAN1%%/bp_seqpart.pl.1.gz
-%%PERL5_MAN1%%/bp_seqret.pl.1.gz
-%%PERL5_MAN1%%/bp_seqretsplit.pl.1.gz
-%%PERL5_MAN1%%/bp_split_seq.pl.1.gz
-%%PERL5_MAN1%%/bp_sreformat.pl.1.gz
-%%PERL5_MAN1%%/bp_taxid4species.pl.1.gz
-%%PERL5_MAN1%%/bp_taxonomy2tree.pl.1.gz
-%%PERL5_MAN1%%/bp_translate_seq.pl.1.gz
-%%PERL5_MAN1%%/bp_tree2pag.pl.1.gz
-%%PERL5_MAN1%%/bp_unflatten_seq.pl.1.gz
-%%DATADIR%%/models/README
-%%DATADIR%%/models/biblio.dia
-%%DATADIR%%/models/bio_liveseq_variation.dia
-%%DATADIR%%/models/bio_map.dia
-%%DATADIR%%/models/bio_restriction.dia
-%%DATADIR%%/models/bioperl.dia
-%%DATADIR%%/models/coordinatemapper.dia
-%%DATADIR%%/models/map_proposal.txt
-%%DATADIR%%/models/maps_and_markers.dia
-%%DATADIR%%/models/popgen.dia
-%%DATADIR%%/models/population_proposal.txt
-%%DATADIR%%/scripts/Bio-DB-GFF/README
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_generate_histogram.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_load_gff.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_meta_gff.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_gadfly.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_sgd.pl
-%%DATADIR%%/scripts/Bio-DB-GFF/bp_process_wormbase.pl
-%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
-%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
-%%DATADIR%%/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
-%%DATADIR%%/scripts/DB-HIV/bp_hivq.pl
-%%DATADIR%%/scripts/DB/TAG
-%%DATADIR%%/scripts/DB/bp_biofetch_genbank_proxy.pl
-%%DATADIR%%/scripts/DB/bp_bioflat_index.pl
-%%DATADIR%%/scripts/DB/bp_biogetseq.pl
-%%DATADIR%%/scripts/DB/bp_flanks.pl
-%%DATADIR%%/scripts/README
-%%DATADIR%%/scripts/das/README
-%%DATADIR%%/scripts/das/TAG
-%%DATADIR%%/scripts/das/bp_das_server.pl
-%%DATADIR%%/scripts/index/TAG
-%%DATADIR%%/scripts/index/bp_fetch.pl
-%%DATADIR%%/scripts/index/bp_index.pl
-%%DATADIR%%/scripts/index/bp_seqret.pl
-%%DATADIR%%/scripts/popgen/bp_composite_LD.pl
-%%DATADIR%%/scripts/popgen/bp_heterogeneity_test.pl
-%%DATADIR%%/scripts/searchio/README
-%%DATADIR%%/scripts/searchio/TAG
-%%DATADIR%%/scripts/searchio/bp_fastam9_to_table.pl
-%%DATADIR%%/scripts/searchio/bp_filter_search.pl
-%%DATADIR%%/scripts/searchio/bp_hmmer_to_table.pl
-%%DATADIR%%/scripts/searchio/bp_parse_hmmsearch.pl
-%%DATADIR%%/scripts/searchio/bp_search2table.pl
-%%DATADIR%%/scripts/seq/TAG
-%%DATADIR%%/scripts/seq/bp_extract_feature_seq.pl
-%%DATADIR%%/scripts/seq/bp_make_mrna_protein.pl
-%%DATADIR%%/scripts/seq/bp_seqconvert.pl
-%%DATADIR%%/scripts/seq/bp_seqcut.pl
-%%DATADIR%%/scripts/seq/bp_seqpart.pl
-%%DATADIR%%/scripts/seq/bp_seqretsplit.pl
-%%DATADIR%%/scripts/seq/bp_split_seq.pl
-%%DATADIR%%/scripts/seq/bp_translate_seq.pl
-%%DATADIR%%/scripts/seq/bp_unflatten_seq.pl
-%%DATADIR%%/scripts/seqstats/TAG
-%%DATADIR%%/scripts/seqstats/bp_aacomp.pl
-%%DATADIR%%/scripts/seqstats/bp_chaos_plot.pl
-%%DATADIR%%/scripts/seqstats/bp_gccalc.pl
-%%DATADIR%%/scripts/seqstats/bp_oligo_count.pl
-%%DATADIR%%/scripts/taxa/TAG
-%%DATADIR%%/scripts/taxa/bp_classify_hits_kingdom.pl
-%%DATADIR%%/scripts/taxa/bp_local_taxonomydb_query.pl
-%%DATADIR%%/scripts/taxa/bp_query_entrez_taxa.pl
-%%DATADIR%%/scripts/taxa/bp_taxid4species.pl
-%%DATADIR%%/scripts/taxa/bp_taxonomy2tree.pl
-%%DATADIR%%/scripts/tree/TAG
-%%DATADIR%%/scripts/tree/bp_blast2tree.pl
-%%DATADIR%%/scripts/tree/bp_nexus2nh.pl
-%%DATADIR%%/scripts/tree/bp_tree2pag.pl
-%%DATADIR%%/scripts/utilities/README
-%%DATADIR%%/scripts/utilities/TAG
-%%DATADIR%%/scripts/utilities/bp_dbsplit.pl
-%%DATADIR%%/scripts/utilities/bp_download_query_genbank.pl
-%%DATADIR%%/scripts/utilities/bp_mask_by_search.pl
-%%DATADIR%%/scripts/utilities/bp_mrtrans.pl
-%%DATADIR%%/scripts/utilities/bp_mutate.pl
-%%DATADIR%%/scripts/utilities/bp_netinstall.pl
-%%DATADIR%%/scripts/utilities/bp_nrdb.pl
-%%DATADIR%%/scripts/utilities/bp_pairwise_kaks.pl
-%%DATADIR%%/scripts/utilities/bp_remote_blast.pl
-%%DATADIR%%/scripts/utilities/bp_revtrans-motif.pl
-%%DATADIR%%/scripts/utilities/bp_search2BSML.pl
-%%DATADIR%%/scripts/utilities/bp_search2alnblocks.pl
-%%DATADIR%%/scripts/utilities/bp_search2gff.pl
-%%DATADIR%%/scripts/utilities/bp_search2tribe.pl
-%%DATADIR%%/scripts/utilities/bp_seq_length.pl
-%%DATADIR%%/scripts/utilities/bp_sreformat.pl
-%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
-%%PORTDOCS%%%%DOCSDIR%%/BUGS
-%%PORTDOCS%%%%DOCSDIR%%/Changes
-%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
-%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL
-%%PORTDOCS%%%%DOCSDIR%%/LICENSE
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