From owner-svn-ports-head@freebsd.org Wed Feb 20 20:46:57 2019 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 8395314DB262; Wed, 20 Feb 2019 20:46:57 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id A3F356CC2E; Wed, 20 Feb 2019 20:46:55 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 658DBAD22; Wed, 20 Feb 2019 20:46:54 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x1KKksv9082373; Wed, 20 Feb 2019 20:46:54 GMT (envelope-from sunpoet@FreeBSD.org) Received: (from sunpoet@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x1KKkr5R082369; Wed, 20 Feb 2019 20:46:53 GMT (envelope-from sunpoet@FreeBSD.org) Message-Id: <201902202046.x1KKkr5R082369@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: sunpoet set sender to sunpoet@FreeBSD.org using -f From: Sunpoet Po-Chuan Hsieh Date: Wed, 20 Feb 2019 20:46:53 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r493447 - in head/biology/p5-BioPerl: . files X-SVN-Group: ports-head X-SVN-Commit-Author: sunpoet X-SVN-Commit-Paths: in head/biology/p5-BioPerl: . files X-SVN-Commit-Revision: 493447 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: A3F356CC2E X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.98)[-0.979,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 20 Feb 2019 20:46:57 -0000 Author: sunpoet Date: Wed Feb 20 20:46:53 2019 New Revision: 493447 URL: https://svnweb.freebsd.org/changeset/ports/493447 Log: Update to 1.007004 (1.7.4) - Add LICENSE_FILE - Use USES=shebangfix - Use COPYTREE_SHARE instead of CP -R - Take maintainership Changes: https://metacpan.org/changes/distribution/BioPerl Deleted: head/biology/p5-BioPerl/files/ Modified: head/biology/p5-BioPerl/Makefile head/biology/p5-BioPerl/distinfo head/biology/p5-BioPerl/pkg-plist Modified: head/biology/p5-BioPerl/Makefile ============================================================================== --- head/biology/p5-BioPerl/Makefile Wed Feb 20 20:46:48 2019 (r493446) +++ head/biology/p5-BioPerl/Makefile Wed Feb 20 20:46:53 2019 (r493447) @@ -2,94 +2,76 @@ # $FreeBSD$ PORTNAME= BioPerl -PORTVERSION= 1.007002 +PORTVERSION= 1.007004 CATEGORIES= biology perl5 MASTER_SITES= CPAN -MASTER_SITE_SUBDIR= CPAN:CJFIELDS +MASTER_SITE_SUBDIR= CPAN:CDRAUG PKGNAMEPREFIX= p5- +DISTNAME= ${PORTNAME}-1.7.4 -MAINTAINER= perl@FreeBSD.org +MAINTAINER= sunpoet@FreeBSD.org COMMENT= Collection of Perl modules for bioinformatics LICENSE= ART10 GPLv1+ LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${RUN_DEPENDS} -RUN_DEPENDS= p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \ - p5-Array-Compare>=0:misc/p5-Array-Compare \ - p5-CGI>=0:www/p5-CGI \ - 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-DBI>=0:databases/p5-DBI \ - p5-Data-Stag>=0.11:devel/p5-Data-Stag \ +RUN_DEPENDS= p5-DBI>=0:databases/p5-DBI \ + p5-Data-Stag>=0:devel/p5-Data-Stag \ p5-Error>=0:lang/p5-Error \ p5-GD>=0:graphics/p5-GD \ - p5-Graph>=0.50:math/p5-Graph \ - p5-GraphViz>=0:graphics/p5-GraphViz \ - p5-HTML-Parser>=3:www/p5-HTML-Parser \ - p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \ + p5-Graph>=0:math/p5-Graph \ 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-Inline-C>=0.67:devel/p5-Inline-C \ + p5-IPC-Run>=0:devel/p5-IPC-Run \ p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \ - p5-PostScript>=0:print/p5-PostScript \ - p5-SVG>=2.26:textproc/p5-SVG \ - p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \ + p5-Module-Build>=0:devel/p5-Module-Build \ p5-Set-Scalar>=0:devel/p5-Set-Scalar \ - p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \ - p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \ - p5-XML-DOM>=0:textproc/p5-XML-DOM \ + p5-Test-Most>=0:devel/p5-Test-Most \ + p5-Test-RequiresInternet>=0:devel/p5-Test-RequiresInternet \ + p5-URI>=0:net/p5-URI \ p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \ + p5-XML-DOM>=0:textproc/p5-XML-DOM \ p5-XML-LibXML>=0:textproc/p5-XML-LibXML \ - p5-XML-Parser>=0:textproc/p5-XML-Parser \ - p5-XML-SAX>=0.15:textproc/p5-XML-SAX \ + p5-XML-SAX-Base>=0:textproc/p5-XML-SAX-Base \ p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \ - p5-XML-Simple>=0:textproc/p5-XML-Simple \ + p5-XML-SAX>=0:textproc/p5-XML-SAX \ p5-XML-Twig>=0:textproc/p5-XML-Twig \ - p5-XML-Writer>=0.400:textproc/p5-XML-Writer \ + p5-XML-Writer>=0:textproc/p5-XML-Writer \ p5-YAML>=0:textproc/p5-YAML \ p5-libwww>=0:www/p5-libwww \ p5-libxml>=0:textproc/p5-libxml -TEST_DEPENDS= p5-Test-Most>=0:devel/p5-Test-Most \ - p5-URI>=0:net/p5-URI +TEST_DEPENDS= p5-Test-Memory-Cycle>=0:devel/p5-Test-Memory-Cycle \ + p5-Test-Weaken>=0:devel/p5-Test-Weaken USES= perl5 shebangfix -USE_PERL5= modbuild +USE_PERL5= configure + NO_ARCH= yes -SHEBANG_FILES= scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl -PORTDATA= * -PORTDOCS= * -PORTEXAMPLES= * - OPTIONS_DEFINE= DOCS EXAMPLES PGTEST SQLITETEST PGTEST_DESC= Test PostGreSQL -SQLITETEST_DESC= Test SQLite +SQLITETEST_DESC=Test SQLite + PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:databases/p5-DBD-Pg 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}/deobfuscator -name "*.pl" -o -name "*.cgi" \ - -o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \ - '1s|(/usr)?/bin/perl|${PERL}|' +SHEBANG_FILES= examples/*.pl examples/*/*.pl post-install: @${MKDIR} ${STAGEDIR}${DATADIR} - ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR} + cd ${WRKSRC}/models && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR} post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md - ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} -.endfor - ${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR} + cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes MANIFEST README.md ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} + cd ${WRKSRC}/examples/ && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include Modified: head/biology/p5-BioPerl/distinfo ============================================================================== --- head/biology/p5-BioPerl/distinfo Wed Feb 20 20:46:48 2019 (r493446) +++ head/biology/p5-BioPerl/distinfo Wed Feb 20 20:46:53 2019 (r493447) @@ -1,3 +1,3 @@ -TIMESTAMP = 1505232617 -SHA256 (BioPerl-1.007002.tar.gz) = 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1 -SIZE (BioPerl-1.007002.tar.gz) = 12362741 +TIMESTAMP = 1549651825 +SHA256 (BioPerl-1.7.4.tar.gz) = 5a074947bba299cdb47cbf1c66689502db02c022fc138459e3393da45d7c707b +SIZE (BioPerl-1.7.4.tar.gz) = 7642013 Modified: head/biology/p5-BioPerl/pkg-plist ============================================================================== --- head/biology/p5-BioPerl/pkg-plist Wed Feb 20 20:46:48 2019 (r493446) +++ head/biology/p5-BioPerl/pkg-plist Wed Feb 20 20:46:53 2019 (r493447) @@ -1,71 +1,47 @@ -bin/bp_aacomp.pl -bin/bp_biofetch_genbank_proxy.pl -bin/bp_bioflat_index.pl -bin/bp_biogetseq.pl -bin/bp_blast2tree.pl -bin/bp_bulk_load_gff.pl -bin/bp_chaos_plot.pl -bin/bp_classify_hits_kingdom.pl -bin/bp_composite_LD.pl -bin/bp_das_server.pl -bin/bp_dbsplit.pl -bin/bp_download_query_genbank.pl -bin/bp_extract_feature_seq.pl -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 -bin/bp_genbank2gff3.pl -bin/bp_generate_histogram.pl -bin/bp_heterogeneity_test.pl -bin/bp_hivq.pl -bin/bp_hmmer_to_table.pl -bin/bp_index.pl -bin/bp_load_gff.pl -bin/bp_local_taxonomydb_query.pl -bin/bp_make_mrna_protein.pl -bin/bp_mask_by_search.pl -bin/bp_meta_gff.pl -bin/bp_mrtrans.pl -bin/bp_mutate.pl -bin/bp_netinstall.pl -bin/bp_nexus2nh.pl -bin/bp_nrdb.pl -bin/bp_oligo_count.pl -bin/bp_parse_hmmsearch.pl -bin/bp_process_gadfly.pl -bin/bp_process_sgd.pl -bin/bp_process_wormbase.pl -bin/bp_query_entrez_taxa.pl -bin/bp_remote_blast.pl -bin/bp_revtrans-motif.pl -bin/bp_search2alnblocks.pl -bin/bp_search2gff.pl -bin/bp_search2table.pl -bin/bp_search2tribe.pl -bin/bp_seq_length.pl -bin/bp_seqconvert.pl -bin/bp_seqcut.pl -bin/bp_seqfeature_delete.pl -bin/bp_seqfeature_gff3.pl -bin/bp_seqfeature_load.pl -bin/bp_seqpart.pl -bin/bp_seqret.pl -bin/bp_seqretsplit.pl -bin/bp_split_seq.pl -bin/bp_sreformat.pl -bin/bp_taxid4species.pl -bin/bp_taxonomy2tree.pl -bin/bp_translate_seq.pl -bin/bp_tree2pag.pl -bin/bp_unflatten_seq.pl +bin/bp_aacomp +bin/bp_bioflat_index +bin/bp_biogetseq +bin/bp_chaos_plot +bin/bp_classify_hits_kingdom +bin/bp_dbsplit +bin/bp_extract_feature_seq +bin/bp_fastam9_to_table +bin/bp_fetch +bin/bp_filter_search +bin/bp_find-blast-matches +bin/bp_gccalc +bin/bp_genbank2gff3 +bin/bp_index +bin/bp_local_taxonomydb_query +bin/bp_make_mrna_protein +bin/bp_mask_by_search +bin/bp_mrtrans +bin/bp_mutate +bin/bp_nexus2nh +bin/bp_nrdb +bin/bp_oligo_count +bin/bp_process_gadfly +bin/bp_process_sgd +bin/bp_revtrans-motif +bin/bp_search2alnblocks +bin/bp_search2gff +bin/bp_search2table +bin/bp_search2tribe +bin/bp_seq_length +bin/bp_seqconvert +bin/bp_seqcut +bin/bp_seqpart +bin/bp_seqret +bin/bp_seqretsplit +bin/bp_split_seq +bin/bp_sreformat +bin/bp_taxid4species +bin/bp_taxonomy2tree +bin/bp_translate_seq +bin/bp_tree2pag +bin/bp_unflatten_seq %%SITE_PERL%%/Bio/Align/AlignI.pm %%SITE_PERL%%/Bio/Align/DNAStatistics.pm -%%SITE_PERL%%/Bio/Align/Graphics.pm %%SITE_PERL%%/Bio/Align/PairwiseStatistics.pm %%SITE_PERL%%/Bio/Align/ProteinStatistics.pm %%SITE_PERL%%/Bio/Align/StatisticsI.pm @@ -84,7 +60,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/AlignIO/meme.pm %%SITE_PERL%%/Bio/AlignIO/metafasta.pm %%SITE_PERL%%/Bio/AlignIO/msf.pm -%%SITE_PERL%%/Bio/AlignIO/nexml.pm %%SITE_PERL%%/Bio/AlignIO/nexus.pm %%SITE_PERL%%/Bio/AlignIO/pfam.pm %%SITE_PERL%%/Bio/AlignIO/phylip.pm @@ -93,7 +68,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/AlignIO/prodom.pm %%SITE_PERL%%/Bio/AlignIO/psi.pm %%SITE_PERL%%/Bio/AlignIO/selex.pm -%%SITE_PERL%%/Bio/AlignIO/stockholm.pm %%SITE_PERL%%/Bio/AlignIO/xmfa.pm %%SITE_PERL%%/Bio/AnalysisI.pm %%SITE_PERL%%/Bio/AnalysisParserI.pm @@ -114,38 +88,9 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Annotation/TypeManager.pm %%SITE_PERL%%/Bio/AnnotationCollectionI.pm %%SITE_PERL%%/Bio/AnnotationI.pm -%%SITE_PERL%%/Bio/Assembly/Contig.pm -%%SITE_PERL%%/Bio/Assembly/ContigAnalysis.pm -%%SITE_PERL%%/Bio/Assembly/IO.pm -%%SITE_PERL%%/Bio/Assembly/IO/ace.pm -%%SITE_PERL%%/Bio/Assembly/IO/bowtie.pm -%%SITE_PERL%%/Bio/Assembly/IO/maq.pm -%%SITE_PERL%%/Bio/Assembly/IO/phrap.pm -%%SITE_PERL%%/Bio/Assembly/IO/sam.pm -%%SITE_PERL%%/Bio/Assembly/IO/tigr.pm -%%SITE_PERL%%/Bio/Assembly/Scaffold.pm -%%SITE_PERL%%/Bio/Assembly/ScaffoldI.pm -%%SITE_PERL%%/Bio/Assembly/Singlet.pm -%%SITE_PERL%%/Bio/Assembly/Tools/ContigSpectrum.pm -%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm -%%SITE_PERL%%/Bio/Cluster/FamilyI.pm -%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm -%%SITE_PERL%%/Bio/Cluster/UniGene.pm -%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm -%%SITE_PERL%%/Bio/ClusterI.pm -%%SITE_PERL%%/Bio/ClusterIO.pm -%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm -%%SITE_PERL%%/Bio/ClusterIO/unigene.pm %%SITE_PERL%%/Bio/CodonUsage/IO.pm %%SITE_PERL%%/Bio/CodonUsage/Table.pm -%%SITE_PERL%%/Bio/DB/Ace.pm -%%SITE_PERL%%/Bio/DB/BioFetch.pm -%%SITE_PERL%%/Bio/DB/CUTG.pm %%SITE_PERL%%/Bio/DB/DBFetch.pm -%%SITE_PERL%%/Bio/DB/EMBL.pm -%%SITE_PERL%%/Bio/DB/EntrezGene.pm -%%SITE_PERL%%/Bio/DB/Expression.pm -%%SITE_PERL%%/Bio/DB/Expression/geo.pm %%SITE_PERL%%/Bio/DB/Failover.pm %%SITE_PERL%%/Bio/DB/Fasta.pm %%SITE_PERL%%/Bio/DB/FileCache.pm @@ -156,108 +101,24 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/DB/Flat/BDB/genbank.pm %%SITE_PERL%%/Bio/DB/Flat/BDB/swiss.pm %%SITE_PERL%%/Bio/DB/Flat/BinarySearch.pm -%%SITE_PERL%%/Bio/DB/GFF.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/ace.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/biofetch_oracle.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/iterator.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysql.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracle.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/oracleace.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm -%%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory/iterator.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/alignment.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/clone.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/coding.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/gene.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/match.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/none.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/orf.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/processed_transcript.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/so_transcript.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/transcript.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_acembly.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_genscan.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_refgene.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_softberry.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm -%%SITE_PERL%%/Bio/DB/GFF/Aggregator/ucsc_unigene.pm -%%SITE_PERL%%/Bio/DB/GFF/Featname.pm -%%SITE_PERL%%/Bio/DB/GFF/Feature.pm -%%SITE_PERL%%/Bio/DB/GFF/Homol.pm -%%SITE_PERL%%/Bio/DB/GFF/RelSegment.pm -%%SITE_PERL%%/Bio/DB/GFF/Segment.pm -%%SITE_PERL%%/Bio/DB/GFF/Typename.pm %%SITE_PERL%%/Bio/DB/GFF/Util/Binning.pm %%SITE_PERL%%/Bio/DB/GFF/Util/Rearrange.pm -%%SITE_PERL%%/Bio/DB/GenBank.pm -%%SITE_PERL%%/Bio/DB/GenPept.pm %%SITE_PERL%%/Bio/DB/GenericWebAgent.pm -%%SITE_PERL%%/Bio/DB/HIV.pm -%%SITE_PERL%%/Bio/DB/HIV/HIVAnnotProcessor.pm -%%SITE_PERL%%/Bio/DB/HIV/HIVQueryHelper.pm -%%SITE_PERL%%/Bio/DB/HIV/lanl-schema.xml %%SITE_PERL%%/Bio/DB/InMemoryCache.pm %%SITE_PERL%%/Bio/DB/IndexedBase.pm %%SITE_PERL%%/Bio/DB/LocationI.pm -%%SITE_PERL%%/Bio/DB/MeSH.pm -%%SITE_PERL%%/Bio/DB/NCBIHelper.pm %%SITE_PERL%%/Bio/DB/Qual.pm -%%SITE_PERL%%/Bio/DB/Query/GenBank.pm -%%SITE_PERL%%/Bio/DB/Query/HIVQuery.pm %%SITE_PERL%%/Bio/DB/Query/WebQuery.pm %%SITE_PERL%%/Bio/DB/QueryI.pm %%SITE_PERL%%/Bio/DB/RandomAccessI.pm -%%SITE_PERL%%/Bio/DB/RefSeq.pm %%SITE_PERL%%/Bio/DB/ReferenceI.pm %%SITE_PERL%%/Bio/DB/Registry.pm -%%SITE_PERL%%/Bio/DB/SeqFeature.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedFeature.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedFeatureI.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Segment.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/Iterator.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/Pg.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/SQLite.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI/mysql.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/GFF2Loader.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/GFF3Loader.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/LoadHelper.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/Loader.pm -%%SITE_PERL%%/Bio/DB/SeqFeature/Store/bdb.pm -%%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/SeqI.pm -%%SITE_PERL%%/Bio/DB/SeqVersion.pm -%%SITE_PERL%%/Bio/DB/SeqVersion/gi.pm -%%SITE_PERL%%/Bio/DB/SwissProt.pm -%%SITE_PERL%%/Bio/DB/TFBS.pm -%%SITE_PERL%%/Bio/DB/TFBS/transfac_pro.pm %%SITE_PERL%%/Bio/DB/Taxonomy.pm -%%SITE_PERL%%/Bio/DB/Taxonomy/entrez.pm %%SITE_PERL%%/Bio/DB/Taxonomy/flatfile.pm %%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 %%SITE_PERL%%/Bio/DBLinkContainerI.pm @@ -265,7 +126,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Das/SegmentI.pm %%SITE_PERL%%/Bio/DasI.pm %%SITE_PERL%%/Bio/DescribableI.pm -%%SITE_PERL%%/Bio/Draw/Pictogram.pm %%SITE_PERL%%/Bio/Event/EventGeneratorI.pm %%SITE_PERL%%/Bio/Event/EventHandlerI.pm %%SITE_PERL%%/Bio/Factory/AnalysisI.pm @@ -273,7 +133,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Factory/DriverFactory.pm %%SITE_PERL%%/Bio/Factory/FTLocationFactory.pm %%SITE_PERL%%/Bio/Factory/LocationFactoryI.pm -%%SITE_PERL%%/Bio/Factory/MapFactoryI.pm %%SITE_PERL%%/Bio/Factory/ObjectBuilderI.pm %%SITE_PERL%%/Bio/Factory/ObjectFactory.pm %%SITE_PERL%%/Bio/Factory/ObjectFactoryI.pm @@ -295,29 +154,9 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Index/Fasta.pm %%SITE_PERL%%/Bio/Index/Fastq.pm %%SITE_PERL%%/Bio/Index/GenBank.pm -%%SITE_PERL%%/Bio/Index/Hmmer.pm %%SITE_PERL%%/Bio/Index/Qual.pm -%%SITE_PERL%%/Bio/Index/Stockholm.pm %%SITE_PERL%%/Bio/Index/SwissPfam.pm %%SITE_PERL%%/Bio/Index/Swissprot.pm -%%SITE_PERL%%/Bio/LiveSeq/AARange.pm -%%SITE_PERL%%/Bio/LiveSeq/Chain.pm -%%SITE_PERL%%/Bio/LiveSeq/ChainI.pm -%%SITE_PERL%%/Bio/LiveSeq/DNA.pm -%%SITE_PERL%%/Bio/LiveSeq/Exon.pm -%%SITE_PERL%%/Bio/LiveSeq/Gene.pm -%%SITE_PERL%%/Bio/LiveSeq/IO/BioPerl.pm -%%SITE_PERL%%/Bio/LiveSeq/IO/Loader.pm -%%SITE_PERL%%/Bio/LiveSeq/Intron.pm -%%SITE_PERL%%/Bio/LiveSeq/Mutation.pm -%%SITE_PERL%%/Bio/LiveSeq/Mutator.pm -%%SITE_PERL%%/Bio/LiveSeq/Prim_Transcript.pm -%%SITE_PERL%%/Bio/LiveSeq/Range.pm -%%SITE_PERL%%/Bio/LiveSeq/Repeat_Region.pm -%%SITE_PERL%%/Bio/LiveSeq/Repeat_Unit.pm -%%SITE_PERL%%/Bio/LiveSeq/SeqI.pm -%%SITE_PERL%%/Bio/LiveSeq/Transcript.pm -%%SITE_PERL%%/Bio/LiveSeq/Translation.pm %%SITE_PERL%%/Bio/LocatableSeq.pm %%SITE_PERL%%/Bio/Location/Atomic.pm %%SITE_PERL%%/Bio/Location/AvWithinCoordPolicy.pm @@ -330,41 +169,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Location/SplitLocationI.pm %%SITE_PERL%%/Bio/Location/WidestCoordPolicy.pm %%SITE_PERL%%/Bio/LocationI.pm -%%SITE_PERL%%/Bio/Map/Clone.pm -%%SITE_PERL%%/Bio/Map/Contig.pm -%%SITE_PERL%%/Bio/Map/CytoMap.pm -%%SITE_PERL%%/Bio/Map/CytoMarker.pm -%%SITE_PERL%%/Bio/Map/CytoPosition.pm -%%SITE_PERL%%/Bio/Map/EntityI.pm -%%SITE_PERL%%/Bio/Map/FPCMarker.pm -%%SITE_PERL%%/Bio/Map/Gene.pm -%%SITE_PERL%%/Bio/Map/GeneMap.pm -%%SITE_PERL%%/Bio/Map/GenePosition.pm -%%SITE_PERL%%/Bio/Map/GeneRelative.pm -%%SITE_PERL%%/Bio/Map/LinkageMap.pm -%%SITE_PERL%%/Bio/Map/LinkagePosition.pm -%%SITE_PERL%%/Bio/Map/MapI.pm -%%SITE_PERL%%/Bio/Map/Mappable.pm -%%SITE_PERL%%/Bio/Map/MappableI.pm -%%SITE_PERL%%/Bio/Map/Marker.pm -%%SITE_PERL%%/Bio/Map/MarkerI.pm -%%SITE_PERL%%/Bio/Map/Microsatellite.pm -%%SITE_PERL%%/Bio/Map/OrderedPosition.pm -%%SITE_PERL%%/Bio/Map/OrderedPositionWithDistance.pm -%%SITE_PERL%%/Bio/Map/Physical.pm -%%SITE_PERL%%/Bio/Map/Position.pm -%%SITE_PERL%%/Bio/Map/PositionHandler.pm -%%SITE_PERL%%/Bio/Map/PositionHandlerI.pm -%%SITE_PERL%%/Bio/Map/PositionI.pm -%%SITE_PERL%%/Bio/Map/PositionWithSequence.pm -%%SITE_PERL%%/Bio/Map/Prediction.pm -%%SITE_PERL%%/Bio/Map/Relative.pm -%%SITE_PERL%%/Bio/Map/RelativeI.pm -%%SITE_PERL%%/Bio/Map/SimpleMap.pm -%%SITE_PERL%%/Bio/Map/TranscriptionFactor.pm -%%SITE_PERL%%/Bio/MapIO.pm -%%SITE_PERL%%/Bio/MapIO/fpc.pm -%%SITE_PERL%%/Bio/MapIO/mapmaker.pm %%SITE_PERL%%/Bio/Matrix/Generic.pm %%SITE_PERL%%/Bio/Matrix/IO.pm %%SITE_PERL%%/Bio/Matrix/IO/mlagan.pm @@ -390,9 +194,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Matrix/PSM/SiteMatrixI.pm %%SITE_PERL%%/Bio/Matrix/PhylipDist.pm %%SITE_PERL%%/Bio/Matrix/Scoring.pm -%%SITE_PERL%%/Bio/MolEvol/CodonModel.pm -%%SITE_PERL%%/Bio/Nexml/Factory.pm -%%SITE_PERL%%/Bio/NexmlIO.pm %%SITE_PERL%%/Bio/Ontology/DocumentRegistry.pm %%SITE_PERL%%/Bio/Ontology/GOterm.pm %%SITE_PERL%%/Bio/Ontology/InterProTerm.pm @@ -424,64 +225,11 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/OntologyIO/simplehierarchy.pm %%SITE_PERL%%/Bio/OntologyIO/soflat.pm %%SITE_PERL%%/Bio/ParameterBaseI.pm -%%SITE_PERL%%/Bio/Perl.pm -%%SITE_PERL%%/Bio/Phenotype/Correlate.pm -%%SITE_PERL%%/Bio/Phenotype/MeSH/Term.pm -%%SITE_PERL%%/Bio/Phenotype/MeSH/Twig.pm -%%SITE_PERL%%/Bio/Phenotype/Measure.pm -%%SITE_PERL%%/Bio/Phenotype/OMIM/MiniMIMentry.pm -%%SITE_PERL%%/Bio/Phenotype/OMIM/OMIMentry.pm -%%SITE_PERL%%/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm -%%SITE_PERL%%/Bio/Phenotype/OMIM/OMIMparser.pm -%%SITE_PERL%%/Bio/Phenotype/Phenotype.pm -%%SITE_PERL%%/Bio/Phenotype/PhenotypeI.pm -%%SITE_PERL%%/Bio/PhyloNetwork.pm -%%SITE_PERL%%/Bio/PhyloNetwork/Factory.pm -%%SITE_PERL%%/Bio/PhyloNetwork/FactoryX.pm -%%SITE_PERL%%/Bio/PhyloNetwork/GraphViz.pm -%%SITE_PERL%%/Bio/PhyloNetwork/RandomFactory.pm -%%SITE_PERL%%/Bio/PhyloNetwork/TreeFactory.pm -%%SITE_PERL%%/Bio/PhyloNetwork/TreeFactoryMulti.pm -%%SITE_PERL%%/Bio/PhyloNetwork/TreeFactoryX.pm -%%SITE_PERL%%/Bio/PhyloNetwork/muVector.pm -%%SITE_PERL%%/Bio/PopGen/Genotype.pm -%%SITE_PERL%%/Bio/PopGen/GenotypeI.pm -%%SITE_PERL%%/Bio/PopGen/HtSNP.pm -%%SITE_PERL%%/Bio/PopGen/IO.pm -%%SITE_PERL%%/Bio/PopGen/IO/csv.pm -%%SITE_PERL%%/Bio/PopGen/IO/hapmap.pm -%%SITE_PERL%%/Bio/PopGen/IO/phase.pm -%%SITE_PERL%%/Bio/PopGen/IO/prettybase.pm -%%SITE_PERL%%/Bio/PopGen/Individual.pm -%%SITE_PERL%%/Bio/PopGen/IndividualI.pm -%%SITE_PERL%%/Bio/PopGen/Marker.pm -%%SITE_PERL%%/Bio/PopGen/MarkerI.pm -%%SITE_PERL%%/Bio/PopGen/PopStats.pm -%%SITE_PERL%%/Bio/PopGen/Population.pm -%%SITE_PERL%%/Bio/PopGen/PopulationI.pm -%%SITE_PERL%%/Bio/PopGen/Simulation/Coalescent.pm -%%SITE_PERL%%/Bio/PopGen/Simulation/GeneticDrift.pm -%%SITE_PERL%%/Bio/PopGen/Statistics.pm -%%SITE_PERL%%/Bio/PopGen/TagHaplotype.pm -%%SITE_PERL%%/Bio/PopGen/Utilities.pm %%SITE_PERL%%/Bio/PrimarySeq.pm %%SITE_PERL%%/Bio/PrimarySeqI.pm %%SITE_PERL%%/Bio/PullParserI.pm %%SITE_PERL%%/Bio/Range.pm %%SITE_PERL%%/Bio/RangeI.pm -%%SITE_PERL%%/Bio/Restriction/Analysis.pm -%%SITE_PERL%%/Bio/Restriction/Enzyme.pm -%%SITE_PERL%%/Bio/Restriction/Enzyme/MultiCut.pm -%%SITE_PERL%%/Bio/Restriction/Enzyme/MultiSite.pm -%%SITE_PERL%%/Bio/Restriction/EnzymeCollection.pm -%%SITE_PERL%%/Bio/Restriction/EnzymeI.pm -%%SITE_PERL%%/Bio/Restriction/IO.pm -%%SITE_PERL%%/Bio/Restriction/IO/bairoch.pm -%%SITE_PERL%%/Bio/Restriction/IO/base.pm -%%SITE_PERL%%/Bio/Restriction/IO/itype2.pm -%%SITE_PERL%%/Bio/Restriction/IO/prototype.pm -%%SITE_PERL%%/Bio/Restriction/IO/withrefm.pm -%%SITE_PERL%%/Bio/Root/Build.pm %%SITE_PERL%%/Bio/Root/Exception.pm %%SITE_PERL%%/Bio/Root/HTTPget.pm %%SITE_PERL%%/Bio/Root/IO.pm @@ -501,10 +249,8 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Search/HSP/BlastPullHSP.pm %%SITE_PERL%%/Bio/Search/HSP/FastaHSP.pm %%SITE_PERL%%/Bio/Search/HSP/GenericHSP.pm -%%SITE_PERL%%/Bio/Search/HSP/HMMERHSP.pm %%SITE_PERL%%/Bio/Search/HSP/HSPFactory.pm %%SITE_PERL%%/Bio/Search/HSP/HSPI.pm -%%SITE_PERL%%/Bio/Search/HSP/HmmpfamHSP.pm %%SITE_PERL%%/Bio/Search/HSP/ModelHSP.pm %%SITE_PERL%%/Bio/Search/HSP/PSLHSP.pm %%SITE_PERL%%/Bio/Search/HSP/PsiBlastHSP.pm @@ -514,14 +260,11 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Search/Hit/BlastPullHit.pm %%SITE_PERL%%/Bio/Search/Hit/Fasta.pm %%SITE_PERL%%/Bio/Search/Hit/GenericHit.pm -%%SITE_PERL%%/Bio/Search/Hit/HMMERHit.pm %%SITE_PERL%%/Bio/Search/Hit/HitFactory.pm %%SITE_PERL%%/Bio/Search/Hit/HitI.pm -%%SITE_PERL%%/Bio/Search/Hit/HmmpfamHit.pm %%SITE_PERL%%/Bio/Search/Hit/ModelHit.pm %%SITE_PERL%%/Bio/Search/Hit/PsiBlastHit.pm %%SITE_PERL%%/Bio/Search/Hit/PullHitI.pm -%%SITE_PERL%%/Bio/Search/Hit/hmmer3Hit.pm %%SITE_PERL%%/Bio/Search/Iteration/GenericIteration.pm %%SITE_PERL%%/Bio/Search/Iteration/IterationI.pm %%SITE_PERL%%/Bio/Search/Processor.pm @@ -529,20 +272,16 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Search/Result/BlastResult.pm %%SITE_PERL%%/Bio/Search/Result/CrossMatchResult.pm %%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 %%SITE_PERL%%/Bio/Search/Result/WABAResult.pm -%%SITE_PERL%%/Bio/Search/Result/hmmer3Result.pm %%SITE_PERL%%/Bio/Search/SearchUtils.pm %%SITE_PERL%%/Bio/Search/StatisticsI.pm %%SITE_PERL%%/Bio/Search/Tiling/MapTileUtils.pm %%SITE_PERL%%/Bio/Search/Tiling/MapTiling.pm %%SITE_PERL%%/Bio/Search/Tiling/TilingI.pm -%%SITE_PERL%%/Bio/SearchDist.pm %%SITE_PERL%%/Bio/SearchIO.pm %%SITE_PERL%%/Bio/SearchIO/EventHandlerI.pm %%SITE_PERL%%/Bio/SearchIO/FastHitEventBuilder.pm @@ -564,10 +303,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/SearchIO/exonerate.pm %%SITE_PERL%%/Bio/SearchIO/fasta.pm %%SITE_PERL%%/Bio/SearchIO/gmap_f9.pm -%%SITE_PERL%%/Bio/SearchIO/hmmer.pm -%%SITE_PERL%%/Bio/SearchIO/hmmer2.pm -%%SITE_PERL%%/Bio/SearchIO/hmmer3.pm -%%SITE_PERL%%/Bio/SearchIO/hmmer_pull.pm %%SITE_PERL%%/Bio/SearchIO/infernal.pm %%SITE_PERL%%/Bio/SearchIO/megablast.pm %%SITE_PERL%%/Bio/SearchIO/psl.pm @@ -599,9 +334,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Seq/SimulatedRead.pm %%SITE_PERL%%/Bio/Seq/TraceI.pm %%SITE_PERL%%/Bio/SeqAnalysisParserI.pm -%%SITE_PERL%%/Bio/SeqEvolution/DNAPoint.pm -%%SITE_PERL%%/Bio/SeqEvolution/EvolutionI.pm -%%SITE_PERL%%/Bio/SeqEvolution/Factory.pm %%SITE_PERL%%/Bio/SeqFeature/Amplicon.pm %%SITE_PERL%%/Bio/SeqFeature/AnnotationAdaptor.pm %%SITE_PERL%%/Bio/SeqFeature/Collection.pm @@ -623,8 +355,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/SeqFeature/Lite.pm %%SITE_PERL%%/Bio/SeqFeature/PositionProxy.pm %%SITE_PERL%%/Bio/SeqFeature/Primer.pm -%%SITE_PERL%%/Bio/SeqFeature/SiRNA/Oligo.pm -%%SITE_PERL%%/Bio/SeqFeature/SiRNA/Pair.pm %%SITE_PERL%%/Bio/SeqFeature/Similarity.pm %%SITE_PERL%%/Bio/SeqFeature/SimilarityPair.pm %%SITE_PERL%%/Bio/SeqFeature/SubSeq.pm @@ -639,25 +369,14 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/SeqIO/FTHelper.pm %%SITE_PERL%%/Bio/SeqIO/Handler/GenericRichSeqHandler.pm %%SITE_PERL%%/Bio/SeqIO/MultiFile.pm -%%SITE_PERL%%/Bio/SeqIO/abi.pm %%SITE_PERL%%/Bio/SeqIO/ace.pm -%%SITE_PERL%%/Bio/SeqIO/agave.pm -%%SITE_PERL%%/Bio/SeqIO/alf.pm %%SITE_PERL%%/Bio/SeqIO/asciitree.pm %%SITE_PERL%%/Bio/SeqIO/bsml.pm %%SITE_PERL%%/Bio/SeqIO/bsml_sax.pm -%%SITE_PERL%%/Bio/SeqIO/chadoxml.pm -%%SITE_PERL%%/Bio/SeqIO/chaos.pm -%%SITE_PERL%%/Bio/SeqIO/chaosxml.pm -%%SITE_PERL%%/Bio/SeqIO/ctf.pm %%SITE_PERL%%/Bio/SeqIO/embl.pm %%SITE_PERL%%/Bio/SeqIO/embldriver.pm -%%SITE_PERL%%/Bio/SeqIO/entrezgene.pm -%%SITE_PERL%%/Bio/SeqIO/excel.pm -%%SITE_PERL%%/Bio/SeqIO/exp.pm %%SITE_PERL%%/Bio/SeqIO/fasta.pm %%SITE_PERL%%/Bio/SeqIO/fastq.pm -%%SITE_PERL%%/Bio/SeqIO/flybase_chadoxml.pm %%SITE_PERL%%/Bio/SeqIO/game.pm %%SITE_PERL%%/Bio/SeqIO/game/featHandler.pm %%SITE_PERL%%/Bio/SeqIO/game/gameHandler.pm @@ -671,20 +390,16 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/SeqIO/interpro.pm %%SITE_PERL%%/Bio/SeqIO/kegg.pm %%SITE_PERL%%/Bio/SeqIO/largefasta.pm -%%SITE_PERL%%/Bio/SeqIO/lasergene.pm %%SITE_PERL%%/Bio/SeqIO/locuslink.pm %%SITE_PERL%%/Bio/SeqIO/mbsout.pm %%SITE_PERL%%/Bio/SeqIO/metafasta.pm %%SITE_PERL%%/Bio/SeqIO/msout.pm -%%SITE_PERL%%/Bio/SeqIO/nexml.pm %%SITE_PERL%%/Bio/SeqIO/phd.pm %%SITE_PERL%%/Bio/SeqIO/pir.pm -%%SITE_PERL%%/Bio/SeqIO/pln.pm %%SITE_PERL%%/Bio/SeqIO/qual.pm %%SITE_PERL%%/Bio/SeqIO/raw.pm %%SITE_PERL%%/Bio/SeqIO/scf.pm %%SITE_PERL%%/Bio/SeqIO/seqxml.pm -%%SITE_PERL%%/Bio/SeqIO/strider.pm %%SITE_PERL%%/Bio/SeqIO/swiss.pm %%SITE_PERL%%/Bio/SeqIO/swissdriver.pm %%SITE_PERL%%/Bio/SeqIO/tab.pm @@ -693,45 +408,21 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/SeqIO/tigrxml.pm %%SITE_PERL%%/Bio/SeqIO/tinyseq.pm %%SITE_PERL%%/Bio/SeqIO/tinyseq/tinyseqHandler.pm -%%SITE_PERL%%/Bio/SeqIO/ztr.pm %%SITE_PERL%%/Bio/SeqUtils.pm %%SITE_PERL%%/Bio/SimpleAlign.pm %%SITE_PERL%%/Bio/SimpleAnalysisI.pm %%SITE_PERL%%/Bio/Species.pm -%%SITE_PERL%%/Bio/Structure/Atom.pm -%%SITE_PERL%%/Bio/Structure/Chain.pm -%%SITE_PERL%%/Bio/Structure/Entry.pm -%%SITE_PERL%%/Bio/Structure/IO.pm -%%SITE_PERL%%/Bio/Structure/IO/pdb.pm -%%SITE_PERL%%/Bio/Structure/Model.pm -%%SITE_PERL%%/Bio/Structure/Residue.pm -%%SITE_PERL%%/Bio/Structure/SecStr/DSSP/Res.pm -%%SITE_PERL%%/Bio/Structure/SecStr/STRIDE/Res.pm -%%SITE_PERL%%/Bio/Structure/StructureI.pm %%SITE_PERL%%/Bio/Symbol/Alphabet.pm %%SITE_PERL%%/Bio/Symbol/AlphabetI.pm %%SITE_PERL%%/Bio/Symbol/DNAAlphabet.pm %%SITE_PERL%%/Bio/Symbol/ProteinAlphabet.pm +%%SITE_PERL%%/Bio/Symbol/README.Symbol %%SITE_PERL%%/Bio/Symbol/Symbol.pm %%SITE_PERL%%/Bio/Symbol/SymbolI.pm %%SITE_PERL%%/Bio/Taxon.pm -%%SITE_PERL%%/Bio/Taxonomy.pm -%%SITE_PERL%%/Bio/Taxonomy/FactoryI.pm -%%SITE_PERL%%/Bio/Taxonomy/Node.pm -%%SITE_PERL%%/Bio/Taxonomy/Taxon.pm -%%SITE_PERL%%/Bio/Taxonomy/Tree.pm -%%SITE_PERL%%/Bio/Tools/AlignFactory.pm %%SITE_PERL%%/Bio/Tools/Alignment/Consed.pm %%SITE_PERL%%/Bio/Tools/Alignment/Trim.pm %%SITE_PERL%%/Bio/Tools/AmpliconSearch.pm -%%SITE_PERL%%/Bio/Tools/Analysis/DNA/ESEfinder.pm -%%SITE_PERL%%/Bio/Tools/Analysis/Protein/Domcut.pm -%%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/NetPhos.pm -%%SITE_PERL%%/Bio/Tools/Analysis/Protein/Scansite.pm -%%SITE_PERL%%/Bio/Tools/Analysis/Protein/Sopma.pm %%SITE_PERL%%/Bio/Tools/Analysis/SimpleAnalysisBase.pm %%SITE_PERL%%/Bio/Tools/AnalysisResult.pm %%SITE_PERL%%/Bio/Tools/Blat.pm @@ -746,7 +437,6 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/Fgenesh.pm %%SITE_PERL%%/Bio/Tools/FootPrinter.pm %%SITE_PERL%%/Bio/Tools/GFF.pm -%%SITE_PERL%%/Bio/Tools/Gel.pm %%SITE_PERL%%/Bio/Tools/Geneid.pm %%SITE_PERL%%/Bio/Tools/Genemark.pm %%SITE_PERL%%/Bio/Tools/Genewise.pm @@ -755,17 +445,12 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/Glimmer.pm %%SITE_PERL%%/Bio/Tools/Grail.pm %%SITE_PERL%%/Bio/Tools/GuessSeqFormat.pm -%%SITE_PERL%%/Bio/Tools/HMMER/Domain.pm -%%SITE_PERL%%/Bio/Tools/HMMER/Results.pm -%%SITE_PERL%%/Bio/Tools/HMMER/Set.pm -%%SITE_PERL%%/Bio/Tools/Hmmpfam.pm %%SITE_PERL%%/Bio/Tools/IUPAC.pm %%SITE_PERL%%/Bio/Tools/Lucy.pm %%SITE_PERL%%/Bio/Tools/MZEF.pm %%SITE_PERL%%/Bio/Tools/Match.pm %%SITE_PERL%%/Bio/Tools/OddCodes.pm %%SITE_PERL%%/Bio/Tools/Phylo/Gerp.pm -%%SITE_PERL%%/Bio/Tools/Phylo/Gumby.pm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy.pm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy/Result.pm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip/ProtDist.pm @@ -780,22 +465,23 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/Profile.pm %%SITE_PERL%%/Bio/Tools/Promoterwise.pm %%SITE_PERL%%/Bio/Tools/PrositeScan.pm -%%SITE_PERL%%/Bio/Tools/Protparam.pm %%SITE_PERL%%/Bio/Tools/Pseudowise.pm %%SITE_PERL%%/Bio/Tools/QRNA.pm %%SITE_PERL%%/Bio/Tools/RandomDistFunctions.pm %%SITE_PERL%%/Bio/Tools/RepeatMasker.pm +%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm +%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.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/Phylo/PhyloBase.pm +%%SITE_PERL%%/Bio/Tools/Run/README +%%SITE_PERL%%/Bio/Tools/Run/WrapperBase.pm +%%SITE_PERL%%/Bio/Tools/Run/WrapperBase/CommandExts.pm %%SITE_PERL%%/Bio/Tools/Seg.pm %%SITE_PERL%%/Bio/Tools/SeqPattern.pm %%SITE_PERL%%/Bio/Tools/SeqPattern/Backtranslate.pm %%SITE_PERL%%/Bio/Tools/SeqStats.pm %%SITE_PERL%%/Bio/Tools/SeqWords.pm -%%SITE_PERL%%/Bio/Tools/SiRNA.pm -%%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset/saigo.pm -%%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset/tuschl.pm %%SITE_PERL%%/Bio/Tools/Sigcleave.pm %%SITE_PERL%%/Bio/Tools/Signalp.pm %%SITE_PERL%%/Bio/Tools/Signalp/ExtendedSignalp.pm @@ -806,17 +492,13 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/Tools/TandemRepeatsFinder.pm %%SITE_PERL%%/Bio/Tools/TargetP.pm %%SITE_PERL%%/Bio/Tools/Tmhmm.pm -%%SITE_PERL%%/Bio/Tools/dpAlign.pm %%SITE_PERL%%/Bio/Tools/ipcress.pm %%SITE_PERL%%/Bio/Tools/isPcr.pm %%SITE_PERL%%/Bio/Tools/pICalculator.pm -%%SITE_PERL%%/Bio/Tools/pSW.pm %%SITE_PERL%%/Bio/Tools/tRNAscanSE.pm -%%SITE_PERL%%/Bio/Tree/AlleleNode.pm %%SITE_PERL%%/Bio/Tree/AnnotatableNode.pm %%SITE_PERL%%/Bio/Tree/Compatible.pm %%SITE_PERL%%/Bio/Tree/DistanceFactory.pm -%%SITE_PERL%%/Bio/Tree/Draw/Cladogram.pm %%SITE_PERL%%/Bio/Tree/Node.pm %%SITE_PERL%%/Bio/Tree/NodeI.pm %%SITE_PERL%%/Bio/Tree/NodeNHX.pm @@ -831,91 +513,58 @@ bin/bp_unflatten_seq.pl %%SITE_PERL%%/Bio/TreeIO/cluster.pm %%SITE_PERL%%/Bio/TreeIO/lintree.pm %%SITE_PERL%%/Bio/TreeIO/newick.pm -%%SITE_PERL%%/Bio/TreeIO/nexml.pm %%SITE_PERL%%/Bio/TreeIO/nexus.pm %%SITE_PERL%%/Bio/TreeIO/nhx.pm %%SITE_PERL%%/Bio/TreeIO/pag.pm %%SITE_PERL%%/Bio/TreeIO/phyloxml.pm -%%SITE_PERL%%/Bio/TreeIO/svggraph.pm %%SITE_PERL%%/Bio/TreeIO/tabtree.pm %%SITE_PERL%%/Bio/UpdateableSeqI.pm -%%SITE_PERL%%/Bio/Variation/AAChange.pm -%%SITE_PERL%%/Bio/Variation/AAReverseMutate.pm -%%SITE_PERL%%/Bio/Variation/Allele.pm -%%SITE_PERL%%/Bio/Variation/DNAMutation.pm -%%SITE_PERL%%/Bio/Variation/IO.pm -%%SITE_PERL%%/Bio/Variation/IO/flat.pm -%%SITE_PERL%%/Bio/Variation/IO/xml.pm -%%SITE_PERL%%/Bio/Variation/RNAChange.pm -%%SITE_PERL%%/Bio/Variation/SNP.pm -%%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_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 +%%SITE_PERL%%/BioPerl.pm +%%PERL5_MAN1%%/bp_aacomp.1.gz +%%PERL5_MAN1%%/bp_bioflat_index.1.gz +%%PERL5_MAN1%%/bp_biogetseq.1.gz +%%PERL5_MAN1%%/bp_chaos_plot.1.gz +%%PERL5_MAN1%%/bp_classify_hits_kingdom.1.gz +%%PERL5_MAN1%%/bp_dbsplit.1.gz +%%PERL5_MAN1%%/bp_extract_feature_seq.1.gz +%%PERL5_MAN1%%/bp_fastam9_to_table.1.gz +%%PERL5_MAN1%%/bp_fetch.1.gz +%%PERL5_MAN1%%/bp_filter_search.1.gz +%%PERL5_MAN1%%/bp_find-blast-matches.1.gz +%%PERL5_MAN1%%/bp_gccalc.1.gz +%%PERL5_MAN1%%/bp_genbank2gff3.1.gz +%%PERL5_MAN1%%/bp_index.1.gz +%%PERL5_MAN1%%/bp_local_taxonomydb_query.1.gz +%%PERL5_MAN1%%/bp_make_mrna_protein.1.gz +%%PERL5_MAN1%%/bp_mask_by_search.1.gz +%%PERL5_MAN1%%/bp_mrtrans.1.gz +%%PERL5_MAN1%%/bp_mutate.1.gz +%%PERL5_MAN1%%/bp_nexus2nh.1.gz +%%PERL5_MAN1%%/bp_nrdb.1.gz +%%PERL5_MAN1%%/bp_oligo_count.1.gz +%%PERL5_MAN1%%/bp_process_gadfly.1.gz +%%PERL5_MAN1%%/bp_process_sgd.1.gz +%%PERL5_MAN1%%/bp_revtrans-motif.1.gz +%%PERL5_MAN1%%/bp_search2alnblocks.1.gz +%%PERL5_MAN1%%/bp_search2gff.1.gz +%%PERL5_MAN1%%/bp_search2table.1.gz +%%PERL5_MAN1%%/bp_search2tribe.1.gz +%%PERL5_MAN1%%/bp_seq_length.1.gz +%%PERL5_MAN1%%/bp_seqconvert.1.gz +%%PERL5_MAN1%%/bp_seqcut.1.gz +%%PERL5_MAN1%%/bp_seqpart.1.gz +%%PERL5_MAN1%%/bp_seqret.1.gz +%%PERL5_MAN1%%/bp_seqretsplit.1.gz +%%PERL5_MAN1%%/bp_split_seq.1.gz +%%PERL5_MAN1%%/bp_sreformat.1.gz +%%PERL5_MAN1%%/bp_taxid4species.1.gz +%%PERL5_MAN1%%/bp_taxonomy2tree.1.gz +%%PERL5_MAN1%%/bp_translate_seq.1.gz +%%PERL5_MAN1%%/bp_tree2pag.1.gz +%%PERL5_MAN1%%/bp_unflatten_seq.1.gz %%PERL5_MAN3%%/Bio::Align::AlignI.3.gz %%PERL5_MAN3%%/Bio::Align::DNAStatistics.3.gz -%%PERL5_MAN3%%/Bio::Align::Graphics.3.gz %%PERL5_MAN3%%/Bio::Align::PairwiseStatistics.3.gz %%PERL5_MAN3%%/Bio::Align::ProteinStatistics.3.gz %%PERL5_MAN3%%/Bio::Align::StatisticsI.3.gz @@ -934,7 +583,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::AlignIO::meme.3.gz %%PERL5_MAN3%%/Bio::AlignIO::metafasta.3.gz %%PERL5_MAN3%%/Bio::AlignIO::msf.3.gz -%%PERL5_MAN3%%/Bio::AlignIO::nexml.3.gz %%PERL5_MAN3%%/Bio::AlignIO::nexus.3.gz %%PERL5_MAN3%%/Bio::AlignIO::pfam.3.gz %%PERL5_MAN3%%/Bio::AlignIO::phylip.3.gz @@ -943,7 +591,6 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::AlignIO::prodom.3.gz %%PERL5_MAN3%%/Bio::AlignIO::psi.3.gz %%PERL5_MAN3%%/Bio::AlignIO::selex.3.gz -%%PERL5_MAN3%%/Bio::AlignIO::stockholm.3.gz %%PERL5_MAN3%%/Bio::AlignIO::xmfa.3.gz %%PERL5_MAN3%%/Bio::AnalysisI.3.gz %%PERL5_MAN3%%/Bio::AnalysisParserI.3.gz @@ -964,38 +611,9 @@ bin/bp_unflatten_seq.pl %%PERL5_MAN3%%/Bio::Annotation::TypeManager.3.gz %%PERL5_MAN3%%/Bio::AnnotationCollectionI.3.gz %%PERL5_MAN3%%/Bio::AnnotationI.3.gz -%%PERL5_MAN3%%/Bio::Assembly::Contig.3.gz -%%PERL5_MAN3%%/Bio::Assembly::ContigAnalysis.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO::ace.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO::bowtie.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO::maq.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO::phrap.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO::sam.3.gz -%%PERL5_MAN3%%/Bio::Assembly::IO::tigr.3.gz -%%PERL5_MAN3%%/Bio::Assembly::Scaffold.3.gz -%%PERL5_MAN3%%/Bio::Assembly::ScaffoldI.3.gz -%%PERL5_MAN3%%/Bio::Assembly::Singlet.3.gz -%%PERL5_MAN3%%/Bio::Assembly::Tools::ContigSpectrum.3.gz -%%PERL5_MAN3%%/Bio::Cluster::ClusterFactory.3.gz -%%PERL5_MAN3%%/Bio::Cluster::FamilyI.3.gz -%%PERL5_MAN3%%/Bio::Cluster::SequenceFamily.3.gz -%%PERL5_MAN3%%/Bio::Cluster::UniGene.3.gz -%%PERL5_MAN3%%/Bio::Cluster::UniGeneI.3.gz -%%PERL5_MAN3%%/Bio::ClusterI.3.gz -%%PERL5_MAN3%%/Bio::ClusterIO.3.gz -%%PERL5_MAN3%%/Bio::ClusterIO::dbsnp.3.gz -%%PERL5_MAN3%%/Bio::ClusterIO::unigene.3.gz %%PERL5_MAN3%%/Bio::CodonUsage::IO.3.gz %%PERL5_MAN3%%/Bio::CodonUsage::Table.3.gz -%%PERL5_MAN3%%/Bio::DB::Ace.3.gz *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***