From 57529925554eea1f70fc30b61f7c0d333af45c31 Mon Sep 17 00:00:00 2001 From: jasper Date: Thu, 16 Dec 2010 12:05:04 +0000 Subject: [PATCH] - update bioperl to 1.6.1 --- biology/bioperl/Makefile | 40 +- biology/bioperl/distinfo | 10 +- .../patches/patch-Bio_Graphics_FeatureFile_pm | 12 - biology/bioperl/patches/patch-INSTALL | 12 - biology/bioperl/patches/patch-Makefile_PL | 12 - .../patch-doc_howto_html_Graphics-HOWTO_html | 21 - .../patch-doc_howto_sgml_Graphics-HOWTO_xml | 14 - .../patch-doc_howto_txt_Graphics-HOWTO_txt | 13 - biology/bioperl/patches/patch-t_BioGraphics_t | 18 - biology/bioperl/pkg/DESCR | 3 +- biology/bioperl/pkg/PLIST | 1289 +++++++++++++++-- 11 files changed, 1180 insertions(+), 264 deletions(-) delete mode 100644 biology/bioperl/patches/patch-Bio_Graphics_FeatureFile_pm delete mode 100644 biology/bioperl/patches/patch-INSTALL delete mode 100644 biology/bioperl/patches/patch-Makefile_PL delete mode 100644 biology/bioperl/patches/patch-doc_howto_html_Graphics-HOWTO_html delete mode 100644 biology/bioperl/patches/patch-doc_howto_sgml_Graphics-HOWTO_xml delete mode 100644 biology/bioperl/patches/patch-doc_howto_txt_Graphics-HOWTO_txt delete mode 100644 biology/bioperl/patches/patch-t_BioGraphics_t diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile index a3f8464f723..026fa843b26 100644 --- a/biology/bioperl/Makefile +++ b/biology/bioperl/Makefile @@ -1,10 +1,9 @@ -# $OpenBSD: Makefile,v 1.8 2010/12/13 10:26:00 jasper Exp $ +# $OpenBSD: Makefile,v 1.9 2010/12/16 12:05:04 jasper Exp $ COMMENT= perl tools for bioinformatics -DISTNAME= bioperl-1.5.0 -PKGNAME= ${DISTNAME} # No p5-prefix here. -REVISION= 1 +DISTNAME= BioPerl-1.6.1 +PKGNAME= ${DISTNAME:L} # No p5-prefix here. CATEGORIES= biology HOMEPAGE= http://bioperl.org/ @@ -21,38 +20,47 @@ MODULES= cpan MODCPAN_EXAMPLES= Yes MODCPAN_EXAMPLES_DIR= ${PREFIX}/share/examples/bioperl/ +CONFIGURE_STYLE=modbuild + +BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= biology/AcePerl \ databases/p5-DBD-mysql \ + converters/p5-Convert-Binary-C \ + devel/p5-Array-Compare \ devel/p5-Class-AutoClass \ devel/p5-Clone \ + devel/p5-Data-Stag \ devel/p5-Graph \ devel/p5-IO-String \ devel/p5-IO-stringy \ + devel/p5-Set-Scalar \ + devel/p5-Test-Exception \ + devel/p5-Tree-DAG_Node \ graphics/p5-GD \ graphics/p5-GD-SVG \ - graphics/p5-SVG \ + graphics/p5-SVG-Graph \ + math/p5-GraphViz \ + textproc/p5-XML-DOM \ textproc/p5-Libxml \ textproc/p5-XML-Parser \ - textproc/p5-XML-SAX \ + textproc/p5-XML-SAX-Writer \ + textproc/p5-XML-Simple \ textproc/p5-XML-Twig \ textproc/p5-XML-Writer \ www/p5-HTML-Parser \ www/p5-SOAP-Lite \ + www/p5-URI \ www/p5-libwww REGRESS_DEPENDS=${RUN_DEPENDS} -# stuff not yet integrated: -# SVG::Graph, Generate optional SVG output, -# (The Bio::TreeIO::svggraph in Bioperl needs it for creating SVG images) -# XML::SAX::Writer, New style SAX parser, -# (The Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax in Bioperl needs it for Writers) -# srsperl, Sequence Retrieval System (SRS) perl -# (needed for API/alternative way of retrieving sequences/Bio::LiveSeq::IO::SRS.pm) +# Optional (not ported) dependencies: +# Algorithm-Munkres +# Postscript-TextBlock +# Spreadsheet-ParseExcel +# Tie-Cacher +# XML-Dom-XPath CONFIGURE_ENV+= PERL_MM_USE_DEFAULT=Yes -pre-configure: - @rm -f ${WRKSRC}/Bio/Graphics/FeatureFile.pm.orig - .include diff --git a/biology/bioperl/distinfo b/biology/bioperl/distinfo index fad1a9a0994..b0fb2026a89 100644 --- a/biology/bioperl/distinfo +++ b/biology/bioperl/distinfo @@ -1,5 +1,5 @@ -MD5 (bioperl-1.5.0.tar.gz) = FyRy8Gdd6aWDQy4hybG1/A== -RMD160 (bioperl-1.5.0.tar.gz) = ErMn6/EJyE5e9RmQ7YRJuuS2FB4= -SHA1 (bioperl-1.5.0.tar.gz) = tVzmHV2kS8AwcwebwaWjgyScyN8= -SHA256 (bioperl-1.5.0.tar.gz) = 835t4S38x7FI0Z2mo/VgkWzufFzNSYN4rlVHMyX+vOo= -SIZE (bioperl-1.5.0.tar.gz) = 6000924 +MD5 (BioPerl-1.6.1.tar.gz) = qojxIsEHFP0nvupLcLZZrQ== +RMD160 (BioPerl-1.6.1.tar.gz) = Rq6CqFSllUhVD/vltpHb7KwbXvU= +SHA1 (BioPerl-1.6.1.tar.gz) = vwjsr6roLCDg4ywTQAUGTpnKQmY= +SHA256 (BioPerl-1.6.1.tar.gz) = rDbazitN2XNWewLM4pFYvqwF/WcocsqHaeArvd3claM= +SIZE (BioPerl-1.6.1.tar.gz) = 10462526 diff --git a/biology/bioperl/patches/patch-Bio_Graphics_FeatureFile_pm b/biology/bioperl/patches/patch-Bio_Graphics_FeatureFile_pm deleted file mode 100644 index 48940aaf354..00000000000 --- a/biology/bioperl/patches/patch-Bio_Graphics_FeatureFile_pm +++ /dev/null @@ -1,12 +0,0 @@ -$OpenBSD: patch-Bio_Graphics_FeatureFile_pm,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- Bio/Graphics/FeatureFile.pm.orig Thu Mar 3 01:16:54 2005 -+++ Bio/Graphics/FeatureFile.pm Thu Mar 3 01:17:17 2005 -@@ -120,7 +120,7 @@ use Bio::DB::GFF::Util::Rearrange; - use Carp; - use Bio::DB::GFF; - use IO::File; --use Text::Shellwords; -+use Text::ParseWords; - - # default colors for unconfigured features - my @COLORS = qw(cyan blue red yellow green wheat turquoise orange); diff --git a/biology/bioperl/patches/patch-INSTALL b/biology/bioperl/patches/patch-INSTALL deleted file mode 100644 index 5c71b8dc783..00000000000 --- a/biology/bioperl/patches/patch-INSTALL +++ /dev/null @@ -1,12 +0,0 @@ -$OpenBSD: patch-INSTALL,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- INSTALL.orig Thu Mar 3 01:16:54 2005 -+++ INSTALL Thu Mar 3 01:17:40 2005 -@@ -485,7 +485,7 @@ o DEPENDENCIES AND Bundle::BioPerl - Storable Persistent object storage & retrieval - Bio::DB::FileCache - -- Text::Shellwords Text parser -+ Text::ParseWords Text parser - Bio::Graphics::FeatureFile - - XML::DOM XML parser diff --git a/biology/bioperl/patches/patch-Makefile_PL b/biology/bioperl/patches/patch-Makefile_PL deleted file mode 100644 index b9a20067c6d..00000000000 --- a/biology/bioperl/patches/patch-Makefile_PL +++ /dev/null @@ -1,12 +0,0 @@ -$OpenBSD: patch-Makefile_PL,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- Makefile.PL.orig Thu Mar 3 01:16:54 2005 -+++ Makefile.PL Thu Mar 3 01:17:04 2005 -@@ -29,7 +29,7 @@ - 'HTML::Parser' => '0.0/HTML parsing/HTML parsing of GDB page/Bio::DB::GDB', - 'DBD::mysql' => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF', - 'GD' => '1.3/Graphical Drawing Toolkit/rendering Sequences and Features/Bio::Graphics', -- 'Text::Shellwords' => '0.0/Execute shell commands/test scripts/Bio::Graphics', -+ 'Text::ParseWords' => '0.0/Execute shell commands/test scripts/Bio::Graphics', - 'SVG' => '2.26/Generate optional SVG output/Bio::Graphics/Bio::Graphics::Pictogram', - 'SVG::Graph' => '0.01/Generate optional SVG output/creating SVG images/Bio::TreeIO::svggraph', - 'GD::SVG' => '0.0/Generate optional SVG output/creating SVG images/Bio::Graphics::Panel', diff --git a/biology/bioperl/patches/patch-doc_howto_html_Graphics-HOWTO_html b/biology/bioperl/patches/patch-doc_howto_html_Graphics-HOWTO_html deleted file mode 100644 index fddc48b16b2..00000000000 --- a/biology/bioperl/patches/patch-doc_howto_html_Graphics-HOWTO_html +++ /dev/null @@ -1,21 +0,0 @@ -$OpenBSD: patch-doc_howto_html_Graphics-HOWTO_html,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- doc/howto/html/Graphics-HOWTO.html.orig Thu Mar 3 01:16:54 2005 -+++ doc/howto/html/Graphics-HOWTO.html Thu Mar 3 01:18:04 2005 -@@ -77,9 +77,7 @@ BioPerl DocBook - around). If you use libgd 2.0.1 or higher, be sure it matches GD - version 2.0.1 or higher. -

-- You will also need to install the Text::Shellwords module, which is -- available from CPAN. --

3. Getting Started

-+

3. Getting Started

- All the code examples and BLAST input files we'll use are available in - the doc/howto/examples/graphics directory in the BioPerl package. -

-@@ -865,4 +863,4 @@ PRES1 127 310 700 - "perldoc Bio::Graphics::Glyph::arrow." -

- BioPerl DocBook --
-\ No newline at end of file -+ diff --git a/biology/bioperl/patches/patch-doc_howto_sgml_Graphics-HOWTO_xml b/biology/bioperl/patches/patch-doc_howto_sgml_Graphics-HOWTO_xml deleted file mode 100644 index 863075934c2..00000000000 --- a/biology/bioperl/patches/patch-doc_howto_sgml_Graphics-HOWTO_xml +++ /dev/null @@ -1,14 +0,0 @@ -$OpenBSD: patch-doc_howto_sgml_Graphics-HOWTO_xml,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- doc/howto/sgml/Graphics-HOWTO.xml.orig Thu Mar 3 01:16:54 2005 -+++ doc/howto/sgml/Graphics-HOWTO.xml Thu Mar 3 01:18:17 2005 -@@ -149,10 +149,6 @@ - version 2.0.1 or higher. - - -- -- You will also need to install the Text::Shellwords module, which is -- available from CPAN. -- - - -
diff --git a/biology/bioperl/patches/patch-doc_howto_txt_Graphics-HOWTO_txt b/biology/bioperl/patches/patch-doc_howto_txt_Graphics-HOWTO_txt deleted file mode 100644 index 90d29bef4b1..00000000000 --- a/biology/bioperl/patches/patch-doc_howto_txt_Graphics-HOWTO_txt +++ /dev/null @@ -1,13 +0,0 @@ -$OpenBSD: patch-doc_howto_txt_Graphics-HOWTO_txt,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- doc/howto/txt/Graphics-HOWTO.txt.orig Thu Mar 3 01:16:54 2005 -+++ doc/howto/txt/Graphics-HOWTO.txt Thu Mar 3 01:18:21 2005 -@@ -95,9 +95,6 @@ Lincoln Stein - around). If you use libgd 2.0.1 or higher, be sure it matches GD - version 2.0.1 or higher. - -- You will also need to install the Text::Shellwords module, which is -- available from CPAN. -- - 3. Getting Started - - All the code examples and BLAST input files we'll use are available in diff --git a/biology/bioperl/patches/patch-t_BioGraphics_t b/biology/bioperl/patches/patch-t_BioGraphics_t deleted file mode 100644 index e0b8fe8616d..00000000000 --- a/biology/bioperl/patches/patch-t_BioGraphics_t +++ /dev/null @@ -1,18 +0,0 @@ -$OpenBSD: patch-t_BioGraphics_t,v 1.1.1.1 2005/03/03 01:42:12 espie Exp $ ---- t/BioGraphics.t.orig Thu Mar 3 01:16:54 2005 -+++ t/BioGraphics.t Thu Mar 3 01:17:24 2005 -@@ -32,12 +32,12 @@ BEGIN { - - eval { - require GD; -- require Text::Shellwords; -+ require Text::ParseWords; - require Bio::Graphics::FeatureFile; - require Bio::Graphics; - }; - if( $@ ) { -- print STDERR "GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.\n"; -+ print STDERR "GD or Text::ParseWords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.\n"; - $error = 1; - } - } diff --git a/biology/bioperl/pkg/DESCR b/biology/bioperl/pkg/DESCR index a10685b2a8e..e2b06251766 100644 --- a/biology/bioperl/pkg/DESCR +++ b/biology/bioperl/pkg/DESCR @@ -1 +1,2 @@ -Bioperl is a package of Perl tools for computational molecular biology. +BioPerl is a toolkit of perl modules useful in building bioinformatics +solutions in Perl. diff --git a/biology/bioperl/pkg/PLIST b/biology/bioperl/pkg/PLIST index 64bc4a3ad7a..c8fd9df18b1 100644 --- a/biology/bioperl/pkg/PLIST +++ b/biology/bioperl/pkg/PLIST @@ -1,4 +1,4 @@ -@comment $OpenBSD: PLIST,v 1.2 2010/12/13 10:26:00 jasper Exp $ +@comment $OpenBSD: PLIST,v 1.3 2010/12/16 12:05:04 jasper Exp $ bin/bp_aacomp.pl bin/bp_biblio.pl bin/bp_biofetch_genbank_proxy.pl @@ -7,27 +7,28 @@ 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_contig_draw.pl bin/bp_dbsplit.pl -bin/bp_embl2picture.pl +bin/bp_download_query_genbank.pl +bin/bp_einfo.pl bin/bp_extract_feature_seq.pl bin/bp_fast_load_gff.pl bin/bp_fastam9_to_table.pl -bin/bp_feature_draw.pl bin/bp_fetch.pl bin/bp_filter_search.pl bin/bp_flanks.pl -bin/bp_frend.pl bin/bp_gccalc.pl bin/bp_genbank2gff.pl bin/bp_genbank2gff3.pl bin/bp_generate_histogram.pl -bin/bp_glyphs2-demo.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 @@ -36,22 +37,29 @@ bin/bp_nexus2nh.pl bin/bp_nrdb.pl bin/bp_oligo_count.pl bin/bp_pairwise_kaks.pl -bin/bp_pg_bulk_load_gff.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_search2BSML.pl bin/bp_search2alnblocks.pl bin/bp_search2gff.pl bin/bp_search2table.pl bin/bp_search2tribe.pl -bin/bp_search_overview.pl bin/bp_seq_length.pl bin/bp_seqconvert.pl +bin/bp_seqfeature_delete.pl +bin/bp_seqfeature_gff3.pl +bin/bp_seqfeature_load.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 @@ -65,6 +73,9 @@ ${P5SITE}/Bio/Align/StatisticsI.pm ${P5SITE}/Bio/Align/Utilities.pm ${P5SITE}/Bio/AlignIO/ ${P5SITE}/Bio/AlignIO.pm +${P5SITE}/Bio/AlignIO/Handler/ +${P5SITE}/Bio/AlignIO/Handler/GenericAlignHandler.pm +${P5SITE}/Bio/AlignIO/arp.pm ${P5SITE}/Bio/AlignIO/bl2seq.pm ${P5SITE}/Bio/AlignIO/clustalw.pm ${P5SITE}/Bio/AlignIO/emboss.pm @@ -80,10 +91,12 @@ ${P5SITE}/Bio/AlignIO/nexus.pm ${P5SITE}/Bio/AlignIO/pfam.pm ${P5SITE}/Bio/AlignIO/phylip.pm ${P5SITE}/Bio/AlignIO/po.pm +${P5SITE}/Bio/AlignIO/proda.pm ${P5SITE}/Bio/AlignIO/prodom.pm ${P5SITE}/Bio/AlignIO/psi.pm ${P5SITE}/Bio/AlignIO/selex.pm ${P5SITE}/Bio/AlignIO/stockholm.pm +${P5SITE}/Bio/AlignIO/xmfa.pm ${P5SITE}/Bio/AnalysisI.pm ${P5SITE}/Bio/AnalysisParserI.pm ${P5SITE}/Bio/AnalysisResultI.pm @@ -95,9 +108,12 @@ ${P5SITE}/Bio/Annotation/Comment.pm ${P5SITE}/Bio/Annotation/DBLink.pm ${P5SITE}/Bio/Annotation/OntologyTerm.pm ${P5SITE}/Bio/Annotation/Reference.pm +${P5SITE}/Bio/Annotation/Relation.pm ${P5SITE}/Bio/Annotation/SimpleValue.pm ${P5SITE}/Bio/Annotation/StructuredValue.pm +${P5SITE}/Bio/Annotation/TagTree.pm ${P5SITE}/Bio/Annotation/Target.pm +${P5SITE}/Bio/Annotation/Tree.pm ${P5SITE}/Bio/Annotation/TypeManager.pm ${P5SITE}/Bio/AnnotationCollectionI.pm ${P5SITE}/Bio/AnnotationI.pm @@ -108,9 +124,12 @@ ${P5SITE}/Bio/Assembly/IO/ ${P5SITE}/Bio/Assembly/IO.pm ${P5SITE}/Bio/Assembly/IO/ace.pm ${P5SITE}/Bio/Assembly/IO/phrap.pm +${P5SITE}/Bio/Assembly/IO/tigr.pm ${P5SITE}/Bio/Assembly/Scaffold.pm ${P5SITE}/Bio/Assembly/ScaffoldI.pm ${P5SITE}/Bio/Assembly/Singlet.pm +${P5SITE}/Bio/Assembly/Tools/ +${P5SITE}/Bio/Assembly/Tools/ContigSpectrum.pm ${P5SITE}/Bio/Biblio/ ${P5SITE}/Bio/Biblio.pm ${P5SITE}/Bio/Biblio/Article.pm @@ -182,6 +201,11 @@ ${P5SITE}/Bio/DB/BioFetch.pm ${P5SITE}/Bio/DB/CUTG.pm ${P5SITE}/Bio/DB/DBFetch.pm ${P5SITE}/Bio/DB/EMBL.pm +${P5SITE}/Bio/DB/EUtilities.pm +${P5SITE}/Bio/DB/EntrezGene.pm +${P5SITE}/Bio/DB/Expression/ +${P5SITE}/Bio/DB/Expression.pm +${P5SITE}/Bio/DB/Expression/geo.pm ${P5SITE}/Bio/DB/Failover.pm ${P5SITE}/Bio/DB/Fasta.pm ${P5SITE}/Bio/DB/FileCache.pm @@ -193,13 +217,14 @@ ${P5SITE}/Bio/DB/Flat/BDB/embl.pm ${P5SITE}/Bio/DB/Flat/BDB/fasta.pm ${P5SITE}/Bio/DB/Flat/BDB/genbank.pm ${P5SITE}/Bio/DB/Flat/BDB/swiss.pm -${P5SITE}/Bio/DB/Flat/BDB/swissprot.pm ${P5SITE}/Bio/DB/Flat/BinarySearch.pm -${P5SITE}/Bio/DB/GDB.pm ${P5SITE}/Bio/DB/GFF/ ${P5SITE}/Bio/DB/GFF.pm ${P5SITE}/Bio/DB/GFF/Adaptor/ ${P5SITE}/Bio/DB/GFF/Adaptor/ace.pm +${P5SITE}/Bio/DB/GFF/Adaptor/berkeleydb/ +${P5SITE}/Bio/DB/GFF/Adaptor/berkeleydb.pm +${P5SITE}/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm ${P5SITE}/Bio/DB/GFF/Adaptor/biofetch.pm ${P5SITE}/Bio/DB/GFF/Adaptor/biofetch_oracle.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/ @@ -208,20 +233,27 @@ ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/iterator.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysql.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm +${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/oracle.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/oracleace.pm ${P5SITE}/Bio/DB/GFF/Adaptor/dbi/pg.pm +${P5SITE}/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm +${P5SITE}/Bio/DB/GFF/Adaptor/memory/ ${P5SITE}/Bio/DB/GFF/Adaptor/memory.pm -${P5SITE}/Bio/DB/GFF/Adaptor/memory_iterator.pm +${P5SITE}/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm +${P5SITE}/Bio/DB/GFF/Adaptor/memory/iterator.pm ${P5SITE}/Bio/DB/GFF/Aggregator/ ${P5SITE}/Bio/DB/GFF/Aggregator.pm ${P5SITE}/Bio/DB/GFF/Aggregator/alignment.pm ${P5SITE}/Bio/DB/GFF/Aggregator/clone.pm ${P5SITE}/Bio/DB/GFF/Aggregator/coding.pm +${P5SITE}/Bio/DB/GFF/Aggregator/gene.pm ${P5SITE}/Bio/DB/GFF/Aggregator/match.pm ${P5SITE}/Bio/DB/GFF/Aggregator/none.pm +${P5SITE}/Bio/DB/GFF/Aggregator/orf.pm ${P5SITE}/Bio/DB/GFF/Aggregator/processed_transcript.pm +${P5SITE}/Bio/DB/GFF/Aggregator/so_transcript.pm ${P5SITE}/Bio/DB/GFF/Aggregator/transcript.pm ${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_acembly.pm ${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm @@ -243,29 +275,65 @@ ${P5SITE}/Bio/DB/GFF/Util/Binning.pm ${P5SITE}/Bio/DB/GFF/Util/Rearrange.pm ${P5SITE}/Bio/DB/GenBank.pm ${P5SITE}/Bio/DB/GenPept.pm +${P5SITE}/Bio/DB/GenericWebAgent.pm +${P5SITE}/Bio/DB/HIV/ +${P5SITE}/Bio/DB/HIV.pm +${P5SITE}/Bio/DB/HIV/HIVAnnotProcessor.pm +${P5SITE}/Bio/DB/HIV/HIVQueryHelper.pm +${P5SITE}/Bio/DB/HIV/lanl-schema.xml ${P5SITE}/Bio/DB/InMemoryCache.pm -${P5SITE}/Bio/DB/MANIFEST -${P5SITE}/Bio/DB/Makefile.PL +${P5SITE}/Bio/DB/LocationI.pm ${P5SITE}/Bio/DB/MeSH.pm ${P5SITE}/Bio/DB/NCBIHelper.pm +${P5SITE}/Bio/DB/Qual.pm ${P5SITE}/Bio/DB/Query/ ${P5SITE}/Bio/DB/Query/GenBank.pm +${P5SITE}/Bio/DB/Query/HIVQuery.pm ${P5SITE}/Bio/DB/Query/WebQuery.pm ${P5SITE}/Bio/DB/QueryI.pm ${P5SITE}/Bio/DB/RandomAccessI.pm ${P5SITE}/Bio/DB/RefSeq.pm +${P5SITE}/Bio/DB/ReferenceI.pm ${P5SITE}/Bio/DB/Registry.pm +${P5SITE}/Bio/DB/SeqFeature/ +${P5SITE}/Bio/DB/SeqFeature.pm +${P5SITE}/Bio/DB/SeqFeature/NormalizedFeature.pm +${P5SITE}/Bio/DB/SeqFeature/NormalizedFeatureI.pm +${P5SITE}/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm +${P5SITE}/Bio/DB/SeqFeature/Segment.pm +${P5SITE}/Bio/DB/SeqFeature/Store/ +${P5SITE}/Bio/DB/SeqFeature/Store.pm +${P5SITE}/Bio/DB/SeqFeature/Store/DBI/ +${P5SITE}/Bio/DB/SeqFeature/Store/DBI/Iterator.pm +${P5SITE}/Bio/DB/SeqFeature/Store/DBI/Pg.pm +${P5SITE}/Bio/DB/SeqFeature/Store/DBI/SQLite.pm +${P5SITE}/Bio/DB/SeqFeature/Store/DBI/mysql.pm +${P5SITE}/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm +${P5SITE}/Bio/DB/SeqFeature/Store/GFF2Loader.pm +${P5SITE}/Bio/DB/SeqFeature/Store/GFF3Loader.pm +${P5SITE}/Bio/DB/SeqFeature/Store/LoadHelper.pm +${P5SITE}/Bio/DB/SeqFeature/Store/Loader.pm +${P5SITE}/Bio/DB/SeqFeature/Store/bdb.pm +${P5SITE}/Bio/DB/SeqFeature/Store/berkeleydb.pm +${P5SITE}/Bio/DB/SeqFeature/Store/berkeleydb3.pm +${P5SITE}/Bio/DB/SeqFeature/Store/memory.pm +${P5SITE}/Bio/DB/SeqHound.pm ${P5SITE}/Bio/DB/SeqI.pm +${P5SITE}/Bio/DB/SeqVersion/ +${P5SITE}/Bio/DB/SeqVersion.pm +${P5SITE}/Bio/DB/SeqVersion/gi.pm ${P5SITE}/Bio/DB/SwissProt.pm +${P5SITE}/Bio/DB/TFBS/ +${P5SITE}/Bio/DB/TFBS.pm +${P5SITE}/Bio/DB/TFBS/transfac_pro.pm ${P5SITE}/Bio/DB/Taxonomy/ ${P5SITE}/Bio/DB/Taxonomy.pm ${P5SITE}/Bio/DB/Taxonomy/entrez.pm ${P5SITE}/Bio/DB/Taxonomy/flatfile.pm +${P5SITE}/Bio/DB/Taxonomy/list.pm ${P5SITE}/Bio/DB/Universal.pm ${P5SITE}/Bio/DB/UpdateableSeqI.pm ${P5SITE}/Bio/DB/WebDBSeqI.pm -${P5SITE}/Bio/DB/XEMBL.pm -${P5SITE}/Bio/DB/XEMBLService.pm ${P5SITE}/Bio/DBLinkContainerI.pm ${P5SITE}/Bio/Das/ ${P5SITE}/Bio/Das/FeatureTypeI.pm @@ -276,24 +344,27 @@ ${P5SITE}/Bio/Event/ ${P5SITE}/Bio/Event/EventGeneratorI.pm ${P5SITE}/Bio/Event/EventHandlerI.pm ${P5SITE}/Bio/Expression/ +${P5SITE}/Bio/Expression/Contact.pm +${P5SITE}/Bio/Expression/DataSet.pm ${P5SITE}/Bio/Expression/FeatureGroup/ ${P5SITE}/Bio/Expression/FeatureGroup.pm ${P5SITE}/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm ${P5SITE}/Bio/Expression/FeatureI.pm ${P5SITE}/Bio/Expression/FeatureSet/ ${P5SITE}/Bio/Expression/FeatureSet/FeatureSetMas50.pm +${P5SITE}/Bio/Expression/Platform.pm +${P5SITE}/Bio/Expression/ProbeI.pm +${P5SITE}/Bio/Expression/Sample.pm ${P5SITE}/Bio/Factory/ ${P5SITE}/Bio/Factory/AnalysisI.pm ${P5SITE}/Bio/Factory/ApplicationFactoryI.pm ${P5SITE}/Bio/Factory/DriverFactory.pm ${P5SITE}/Bio/Factory/FTLocationFactory.pm -${P5SITE}/Bio/Factory/HitFactoryI.pm ${P5SITE}/Bio/Factory/LocationFactoryI.pm ${P5SITE}/Bio/Factory/MapFactoryI.pm ${P5SITE}/Bio/Factory/ObjectBuilderI.pm ${P5SITE}/Bio/Factory/ObjectFactory.pm ${P5SITE}/Bio/Factory/ObjectFactoryI.pm -${P5SITE}/Bio/Factory/ResultFactoryI.pm ${P5SITE}/Bio/Factory/SeqAnalysisParserFactory.pm ${P5SITE}/Bio/Factory/SeqAnalysisParserFactoryI.pm ${P5SITE}/Bio/Factory/SequenceFactoryI.pm @@ -307,95 +378,23 @@ ${P5SITE}/Bio/FeatureIO/bed.pm ${P5SITE}/Bio/FeatureIO/gff.pm ${P5SITE}/Bio/FeatureIO/gtf.pm ${P5SITE}/Bio/FeatureIO/interpro.pm -${P5SITE}/Bio/Graph/ -${P5SITE}/Bio/Graph/Edge.pm -${P5SITE}/Bio/Graph/IO/ -${P5SITE}/Bio/Graph/IO.pm -${P5SITE}/Bio/Graph/IO/dip.pm -${P5SITE}/Bio/Graph/IO/psi_xml.pm -${P5SITE}/Bio/Graph/ProteinGraph.pm -${P5SITE}/Bio/Graph/SimpleGraph/ -${P5SITE}/Bio/Graph/SimpleGraph.pm -${P5SITE}/Bio/Graph/SimpleGraph/Traversal.pm -${P5SITE}/Bio/Graphics/ -${P5SITE}/Bio/Graphics.pm -${P5SITE}/Bio/Graphics/ConfiguratorI.pm -${P5SITE}/Bio/Graphics/Feature.pm -${P5SITE}/Bio/Graphics/FeatureFile/ -${P5SITE}/Bio/Graphics/FeatureFile.pm -${P5SITE}/Bio/Graphics/FeatureFile/Iterator.pm -${P5SITE}/Bio/Graphics/Glyph/ -${P5SITE}/Bio/Graphics/Glyph.pm -${P5SITE}/Bio/Graphics/Glyph/Factory.pm -${P5SITE}/Bio/Graphics/Glyph/alignment.pm -${P5SITE}/Bio/Graphics/Glyph/anchored_arrow.pm -${P5SITE}/Bio/Graphics/Glyph/arrow.pm -${P5SITE}/Bio/Graphics/Glyph/box.pm -${P5SITE}/Bio/Graphics/Glyph/broken_line.pm -${P5SITE}/Bio/Graphics/Glyph/cds.pm -${P5SITE}/Bio/Graphics/Glyph/christmas_arrow.pm -${P5SITE}/Bio/Graphics/Glyph/crossbox.pm -${P5SITE}/Bio/Graphics/Glyph/dashed_line.pm -${P5SITE}/Bio/Graphics/Glyph/diamond.pm -${P5SITE}/Bio/Graphics/Glyph/dna.pm -${P5SITE}/Bio/Graphics/Glyph/dot.pm -${P5SITE}/Bio/Graphics/Glyph/dumbbell.pm -${P5SITE}/Bio/Graphics/Glyph/ellipse.pm -${P5SITE}/Bio/Graphics/Glyph/ex.pm -${P5SITE}/Bio/Graphics/Glyph/extending_arrow.pm -${P5SITE}/Bio/Graphics/Glyph/flag.pm -${P5SITE}/Bio/Graphics/Glyph/generic.pm -${P5SITE}/Bio/Graphics/Glyph/graded_segments.pm -${P5SITE}/Bio/Graphics/Glyph/group.pm -${P5SITE}/Bio/Graphics/Glyph/heterogeneous_segments.pm -${P5SITE}/Bio/Graphics/Glyph/lightning.pm -${P5SITE}/Bio/Graphics/Glyph/line.pm -${P5SITE}/Bio/Graphics/Glyph/minmax.pm -${P5SITE}/Bio/Graphics/Glyph/oval.pm -${P5SITE}/Bio/Graphics/Glyph/pentagram.pm -${P5SITE}/Bio/Graphics/Glyph/pinsertion.pm -${P5SITE}/Bio/Graphics/Glyph/primers.pm -${P5SITE}/Bio/Graphics/Glyph/processed_transcript.pm -${P5SITE}/Bio/Graphics/Glyph/ragged_ends.pm -${P5SITE}/Bio/Graphics/Glyph/redgreen_box.pm -${P5SITE}/Bio/Graphics/Glyph/redgreen_segment.pm -${P5SITE}/Bio/Graphics/Glyph/repeating_shape.pm -${P5SITE}/Bio/Graphics/Glyph/rndrect.pm -${P5SITE}/Bio/Graphics/Glyph/ruler_arrow.pm -${P5SITE}/Bio/Graphics/Glyph/saw_teeth.pm -${P5SITE}/Bio/Graphics/Glyph/segmented_keyglyph.pm -${P5SITE}/Bio/Graphics/Glyph/segments.pm -${P5SITE}/Bio/Graphics/Glyph/span.pm -${P5SITE}/Bio/Graphics/Glyph/splice_site.pm -${P5SITE}/Bio/Graphics/Glyph/text_in_box.pm -${P5SITE}/Bio/Graphics/Glyph/three_letters.pm -${P5SITE}/Bio/Graphics/Glyph/tic_tac_toe.pm -${P5SITE}/Bio/Graphics/Glyph/toomany.pm -${P5SITE}/Bio/Graphics/Glyph/track.pm -${P5SITE}/Bio/Graphics/Glyph/transcript.pm -${P5SITE}/Bio/Graphics/Glyph/transcript2.pm -${P5SITE}/Bio/Graphics/Glyph/translation.pm -${P5SITE}/Bio/Graphics/Glyph/triangle.pm -${P5SITE}/Bio/Graphics/Glyph/two_bolts.pm -${P5SITE}/Bio/Graphics/Glyph/wave.pm -${P5SITE}/Bio/Graphics/Glyph/weighted_arrow.pm -${P5SITE}/Bio/Graphics/Glyph/xyplot.pm -${P5SITE}/Bio/Graphics/Panel.pm -${P5SITE}/Bio/Graphics/Pictogram.pm -${P5SITE}/Bio/Graphics/RendererI.pm -${P5SITE}/Bio/Graphics/Util.pm +${P5SITE}/Bio/FeatureIO/ptt.pm +${P5SITE}/Bio/FeatureIO/vecscreen_simple.pm +${P5SITE}/Bio/HandlerBaseI.pm ${P5SITE}/Bio/IdCollectionI.pm ${P5SITE}/Bio/IdentifiableI.pm ${P5SITE}/Bio/Index/ ${P5SITE}/Bio/Index/Abstract.pm ${P5SITE}/Bio/Index/AbstractSeq.pm ${P5SITE}/Bio/Index/Blast.pm +${P5SITE}/Bio/Index/BlastTable.pm ${P5SITE}/Bio/Index/EMBL.pm ${P5SITE}/Bio/Index/Fasta.pm ${P5SITE}/Bio/Index/Fastq.pm ${P5SITE}/Bio/Index/GenBank.pm ${P5SITE}/Bio/Index/Hmmer.pm ${P5SITE}/Bio/Index/Qual.pm +${P5SITE}/Bio/Index/Stockholm.pm ${P5SITE}/Bio/Index/SwissPfam.pm ${P5SITE}/Bio/Index/Swissprot.pm ${P5SITE}/Bio/LiveSeq/ @@ -408,8 +407,6 @@ ${P5SITE}/Bio/LiveSeq/Gene.pm ${P5SITE}/Bio/LiveSeq/IO/ ${P5SITE}/Bio/LiveSeq/IO/BioPerl.pm ${P5SITE}/Bio/LiveSeq/IO/Loader.pm -${P5SITE}/Bio/LiveSeq/IO/README -${P5SITE}/Bio/LiveSeq/IO/SRS.pm ${P5SITE}/Bio/LiveSeq/Intron.pm ${P5SITE}/Bio/LiveSeq/Mutation.pm ${P5SITE}/Bio/LiveSeq/Mutator.pm @@ -439,10 +436,16 @@ ${P5SITE}/Bio/Map/Contig.pm ${P5SITE}/Bio/Map/CytoMap.pm ${P5SITE}/Bio/Map/CytoMarker.pm ${P5SITE}/Bio/Map/CytoPosition.pm +${P5SITE}/Bio/Map/EntityI.pm ${P5SITE}/Bio/Map/FPCMarker.pm +${P5SITE}/Bio/Map/Gene.pm +${P5SITE}/Bio/Map/GeneMap.pm +${P5SITE}/Bio/Map/GenePosition.pm +${P5SITE}/Bio/Map/GeneRelative.pm ${P5SITE}/Bio/Map/LinkageMap.pm ${P5SITE}/Bio/Map/LinkagePosition.pm ${P5SITE}/Bio/Map/MapI.pm +${P5SITE}/Bio/Map/Mappable.pm ${P5SITE}/Bio/Map/MappableI.pm ${P5SITE}/Bio/Map/Marker.pm ${P5SITE}/Bio/Map/MarkerI.pm @@ -451,8 +454,15 @@ ${P5SITE}/Bio/Map/OrderedPosition.pm ${P5SITE}/Bio/Map/OrderedPositionWithDistance.pm ${P5SITE}/Bio/Map/Physical.pm ${P5SITE}/Bio/Map/Position.pm +${P5SITE}/Bio/Map/PositionHandler.pm +${P5SITE}/Bio/Map/PositionHandlerI.pm ${P5SITE}/Bio/Map/PositionI.pm +${P5SITE}/Bio/Map/PositionWithSequence.pm +${P5SITE}/Bio/Map/Prediction.pm +${P5SITE}/Bio/Map/Relative.pm +${P5SITE}/Bio/Map/RelativeI.pm ${P5SITE}/Bio/Map/SimpleMap.pm +${P5SITE}/Bio/Map/TranscriptionFactor.pm ${P5SITE}/Bio/MapIO/ ${P5SITE}/Bio/MapIO.pm ${P5SITE}/Bio/MapIO/fpc.pm @@ -461,9 +471,11 @@ ${P5SITE}/Bio/Matrix/ ${P5SITE}/Bio/Matrix/Generic.pm ${P5SITE}/Bio/Matrix/IO/ ${P5SITE}/Bio/Matrix/IO.pm +${P5SITE}/Bio/Matrix/IO/mlagan.pm ${P5SITE}/Bio/Matrix/IO/phylip.pm ${P5SITE}/Bio/Matrix/IO/scoring.pm ${P5SITE}/Bio/Matrix/MatrixI.pm +${P5SITE}/Bio/Matrix/Mlagan.pm ${P5SITE}/Bio/Matrix/PSM/ ${P5SITE}/Bio/Matrix/PSM/IO/ ${P5SITE}/Bio/Matrix/PSM/IO.pm @@ -484,10 +496,14 @@ ${P5SITE}/Bio/Matrix/PSM/SiteMatrix.pm ${P5SITE}/Bio/Matrix/PSM/SiteMatrixI.pm ${P5SITE}/Bio/Matrix/PhylipDist.pm ${P5SITE}/Bio/Matrix/Scoring.pm +${P5SITE}/Bio/MolEvol/ +${P5SITE}/Bio/MolEvol/CodonModel.pm ${P5SITE}/Bio/Ontology/ ${P5SITE}/Bio/Ontology/DocumentRegistry.pm ${P5SITE}/Bio/Ontology/GOterm.pm ${P5SITE}/Bio/Ontology/InterProTerm.pm +${P5SITE}/Bio/Ontology/OBOEngine.pm +${P5SITE}/Bio/Ontology/OBOterm.pm ${P5SITE}/Bio/Ontology/Ontology.pm ${P5SITE}/Bio/Ontology/OntologyEngineI.pm ${P5SITE}/Bio/Ontology/OntologyI.pm @@ -498,7 +514,9 @@ ${P5SITE}/Bio/Ontology/Relationship.pm ${P5SITE}/Bio/Ontology/RelationshipFactory.pm ${P5SITE}/Bio/Ontology/RelationshipI.pm ${P5SITE}/Bio/Ontology/RelationshipType.pm -${P5SITE}/Bio/Ontology/SimpleGOEngine.pm +${P5SITE}/Bio/Ontology/SimpleGOEngine/ +${P5SITE}/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm +${P5SITE}/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm ${P5SITE}/Bio/Ontology/SimpleOntologyEngine.pm ${P5SITE}/Bio/Ontology/Term.pm ${P5SITE}/Bio/Ontology/TermFactory.pm @@ -512,8 +530,10 @@ ${P5SITE}/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm ${P5SITE}/Bio/OntologyIO/InterProParser.pm ${P5SITE}/Bio/OntologyIO/dagflat.pm ${P5SITE}/Bio/OntologyIO/goflat.pm +${P5SITE}/Bio/OntologyIO/obo.pm ${P5SITE}/Bio/OntologyIO/simplehierarchy.pm ${P5SITE}/Bio/OntologyIO/soflat.pm +${P5SITE}/Bio/ParameterBaseI.pm ${P5SITE}/Bio/Perl.pm ${P5SITE}/Bio/Phenotype/ ${P5SITE}/Bio/Phenotype/Correlate.pm @@ -528,6 +548,16 @@ ${P5SITE}/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm ${P5SITE}/Bio/Phenotype/OMIM/OMIMparser.pm ${P5SITE}/Bio/Phenotype/Phenotype.pm ${P5SITE}/Bio/Phenotype/PhenotypeI.pm +${P5SITE}/Bio/PhyloNetwork/ +${P5SITE}/Bio/PhyloNetwork.pm +${P5SITE}/Bio/PhyloNetwork/Factory.pm +${P5SITE}/Bio/PhyloNetwork/FactoryX.pm +${P5SITE}/Bio/PhyloNetwork/GraphViz.pm +${P5SITE}/Bio/PhyloNetwork/RandomFactory.pm +${P5SITE}/Bio/PhyloNetwork/TreeFactory.pm +${P5SITE}/Bio/PhyloNetwork/TreeFactoryMulti.pm +${P5SITE}/Bio/PhyloNetwork/TreeFactoryX.pm +${P5SITE}/Bio/PhyloNetwork/muVector.pm ${P5SITE}/Bio/PopGen/ ${P5SITE}/Bio/PopGen/Genotype.pm ${P5SITE}/Bio/PopGen/GenotypeI.pm @@ -553,6 +583,7 @@ ${P5SITE}/Bio/PopGen/TagHaplotype.pm ${P5SITE}/Bio/PopGen/Utilities.pm ${P5SITE}/Bio/PrimarySeq.pm ${P5SITE}/Bio/PrimarySeqI.pm +${P5SITE}/Bio/PullParserI.pm ${P5SITE}/Bio/Range.pm ${P5SITE}/Bio/RangeI.pm ${P5SITE}/Bio/Restriction/ @@ -568,22 +599,21 @@ ${P5SITE}/Bio/Restriction/IO.pm ${P5SITE}/Bio/Restriction/IO/bairoch.pm ${P5SITE}/Bio/Restriction/IO/base.pm ${P5SITE}/Bio/Restriction/IO/itype2.pm +${P5SITE}/Bio/Restriction/IO/prototype.pm ${P5SITE}/Bio/Restriction/IO/withrefm.pm ${P5SITE}/Bio/Root/ -${P5SITE}/Bio/Root/Err.pm +${P5SITE}/Bio/Root/Build.pm ${P5SITE}/Bio/Root/Exception.pm -${P5SITE}/Bio/Root/Global.pm ${P5SITE}/Bio/Root/HTTPget.pm ${P5SITE}/Bio/Root/IO.pm -${P5SITE}/Bio/Root/IOManager.pm -${P5SITE}/Bio/Root/Object.pm ${P5SITE}/Bio/Root/Root.pm ${P5SITE}/Bio/Root/RootI.pm ${P5SITE}/Bio/Root/Storable.pm +${P5SITE}/Bio/Root/Test/ +${P5SITE}/Bio/Root/Test.pm +${P5SITE}/Bio/Root/Test/Warn.pm ${P5SITE}/Bio/Root/Utilities.pm -${P5SITE}/Bio/Root/Vector.pm ${P5SITE}/Bio/Root/Version.pm -${P5SITE}/Bio/Root/Xref.pm ${P5SITE}/Bio/Search/ ${P5SITE}/Bio/Search/BlastStatistics.pm ${P5SITE}/Bio/Search/BlastUtils.pm @@ -592,35 +622,51 @@ ${P5SITE}/Bio/Search/GenericDatabase.pm ${P5SITE}/Bio/Search/GenericStatistics.pm ${P5SITE}/Bio/Search/HSP/ ${P5SITE}/Bio/Search/HSP/BlastHSP.pm +${P5SITE}/Bio/Search/HSP/BlastPullHSP.pm ${P5SITE}/Bio/Search/HSP/FastaHSP.pm ${P5SITE}/Bio/Search/HSP/GenericHSP.pm ${P5SITE}/Bio/Search/HSP/HMMERHSP.pm ${P5SITE}/Bio/Search/HSP/HSPFactory.pm ${P5SITE}/Bio/Search/HSP/HSPI.pm +${P5SITE}/Bio/Search/HSP/HmmpfamHSP.pm +${P5SITE}/Bio/Search/HSP/ModelHSP.pm ${P5SITE}/Bio/Search/HSP/PSLHSP.pm ${P5SITE}/Bio/Search/HSP/PsiBlastHSP.pm +${P5SITE}/Bio/Search/HSP/PullHSPI.pm ${P5SITE}/Bio/Search/HSP/WABAHSP.pm ${P5SITE}/Bio/Search/Hit/ ${P5SITE}/Bio/Search/Hit/BlastHit.pm +${P5SITE}/Bio/Search/Hit/BlastPullHit.pm ${P5SITE}/Bio/Search/Hit/Fasta.pm ${P5SITE}/Bio/Search/Hit/GenericHit.pm ${P5SITE}/Bio/Search/Hit/HMMERHit.pm ${P5SITE}/Bio/Search/Hit/HitFactory.pm ${P5SITE}/Bio/Search/Hit/HitI.pm +${P5SITE}/Bio/Search/Hit/HmmpfamHit.pm +${P5SITE}/Bio/Search/Hit/ModelHit.pm ${P5SITE}/Bio/Search/Hit/PsiBlastHit.pm +${P5SITE}/Bio/Search/Hit/PullHitI.pm ${P5SITE}/Bio/Search/Iteration/ ${P5SITE}/Bio/Search/Iteration/GenericIteration.pm ${P5SITE}/Bio/Search/Iteration/IterationI.pm ${P5SITE}/Bio/Search/Processor.pm ${P5SITE}/Bio/Search/Result/ +${P5SITE}/Bio/Search/Result/BlastPullResult.pm ${P5SITE}/Bio/Search/Result/BlastResult.pm +${P5SITE}/Bio/Search/Result/CrossMatchResult.pm ${P5SITE}/Bio/Search/Result/GenericResult.pm ${P5SITE}/Bio/Search/Result/HMMERResult.pm +${P5SITE}/Bio/Search/Result/HmmpfamResult.pm +${P5SITE}/Bio/Search/Result/PullResultI.pm ${P5SITE}/Bio/Search/Result/ResultFactory.pm ${P5SITE}/Bio/Search/Result/ResultI.pm ${P5SITE}/Bio/Search/Result/WABAResult.pm ${P5SITE}/Bio/Search/SearchUtils.pm ${P5SITE}/Bio/Search/StatisticsI.pm +${P5SITE}/Bio/Search/Tiling/ +${P5SITE}/Bio/Search/Tiling/MapTileUtils.pm +${P5SITE}/Bio/Search/Tiling/MapTiling.pm +${P5SITE}/Bio/Search/Tiling/TilingI.pm ${P5SITE}/Bio/SearchDist.pm ${P5SITE}/Bio/SearchIO/ ${P5SITE}/Bio/SearchIO.pm @@ -637,15 +683,25 @@ ${P5SITE}/Bio/SearchIO/Writer/HTMLResultWriter.pm ${P5SITE}/Bio/SearchIO/Writer/HitTableWriter.pm ${P5SITE}/Bio/SearchIO/Writer/ResultTableWriter.pm ${P5SITE}/Bio/SearchIO/Writer/TextResultWriter.pm +${P5SITE}/Bio/SearchIO/XML/ +${P5SITE}/Bio/SearchIO/XML/BlastHandler.pm +${P5SITE}/Bio/SearchIO/XML/PsiBlastHandler.pm ${P5SITE}/Bio/SearchIO/axt.pm ${P5SITE}/Bio/SearchIO/blast.pm +${P5SITE}/Bio/SearchIO/blast_pull.pm ${P5SITE}/Bio/SearchIO/blasttable.pm ${P5SITE}/Bio/SearchIO/blastxml.pm +${P5SITE}/Bio/SearchIO/cross_match.pm +${P5SITE}/Bio/SearchIO/erpin.pm ${P5SITE}/Bio/SearchIO/exonerate.pm ${P5SITE}/Bio/SearchIO/fasta.pm +${P5SITE}/Bio/SearchIO/gmap_f9.pm ${P5SITE}/Bio/SearchIO/hmmer.pm +${P5SITE}/Bio/SearchIO/hmmer_pull.pm +${P5SITE}/Bio/SearchIO/infernal.pm ${P5SITE}/Bio/SearchIO/megablast.pm ${P5SITE}/Bio/SearchIO/psl.pm +${P5SITE}/Bio/SearchIO/rnamotif.pm ${P5SITE}/Bio/SearchIO/sim4.pm ${P5SITE}/Bio/SearchIO/waba.pm ${P5SITE}/Bio/SearchIO/wise.pm @@ -664,6 +720,7 @@ ${P5SITE}/Bio/Seq/MetaI.pm ${P5SITE}/Bio/Seq/PrimaryQual.pm ${P5SITE}/Bio/Seq/PrimedSeq.pm ${P5SITE}/Bio/Seq/QualI.pm +${P5SITE}/Bio/Seq/Quality.pm ${P5SITE}/Bio/Seq/RichSeq.pm ${P5SITE}/Bio/Seq/RichSeqI.pm ${P5SITE}/Bio/Seq/SeqBuilder.pm @@ -673,6 +730,10 @@ ${P5SITE}/Bio/Seq/SeqWithQuality.pm ${P5SITE}/Bio/Seq/SequenceTrace.pm ${P5SITE}/Bio/Seq/TraceI.pm ${P5SITE}/Bio/SeqAnalysisParserI.pm +${P5SITE}/Bio/SeqEvolution/ +${P5SITE}/Bio/SeqEvolution/DNAPoint.pm +${P5SITE}/Bio/SeqEvolution/EvolutionI.pm +${P5SITE}/Bio/SeqEvolution/Factory.pm ${P5SITE}/Bio/SeqFeature/ ${P5SITE}/Bio/SeqFeature/Annotated.pm ${P5SITE}/Bio/SeqFeature/AnnotationAdaptor.pm @@ -693,6 +754,7 @@ ${P5SITE}/Bio/SeqFeature/Gene/Transcript.pm ${P5SITE}/Bio/SeqFeature/Gene/TranscriptI.pm ${P5SITE}/Bio/SeqFeature/Gene/UTR.pm ${P5SITE}/Bio/SeqFeature/Generic.pm +${P5SITE}/Bio/SeqFeature/Lite.pm ${P5SITE}/Bio/SeqFeature/PositionProxy.pm ${P5SITE}/Bio/SeqFeature/Primer.pm ${P5SITE}/Bio/SeqFeature/SiRNA/ @@ -705,11 +767,14 @@ ${P5SITE}/Bio/SeqFeature/Tools/FeatureNamer.pm ${P5SITE}/Bio/SeqFeature/Tools/IDHandler.pm ${P5SITE}/Bio/SeqFeature/Tools/TypeMapper.pm ${P5SITE}/Bio/SeqFeature/Tools/Unflattener.pm +${P5SITE}/Bio/SeqFeature/TypedSeqFeatureI.pm ${P5SITE}/Bio/SeqFeatureI.pm ${P5SITE}/Bio/SeqI.pm ${P5SITE}/Bio/SeqIO/ ${P5SITE}/Bio/SeqIO.pm ${P5SITE}/Bio/SeqIO/FTHelper.pm +${P5SITE}/Bio/SeqIO/Handler/ +${P5SITE}/Bio/SeqIO/Handler/GenericRichSeqHandler.pm ${P5SITE}/Bio/SeqIO/MultiFile.pm ${P5SITE}/Bio/SeqIO/abi.pm ${P5SITE}/Bio/SeqIO/ace.pm @@ -723,9 +788,13 @@ ${P5SITE}/Bio/SeqIO/chaos.pm ${P5SITE}/Bio/SeqIO/chaosxml.pm ${P5SITE}/Bio/SeqIO/ctf.pm ${P5SITE}/Bio/SeqIO/embl.pm +${P5SITE}/Bio/SeqIO/embldriver.pm +${P5SITE}/Bio/SeqIO/entrezgene.pm +${P5SITE}/Bio/SeqIO/excel.pm ${P5SITE}/Bio/SeqIO/exp.pm ${P5SITE}/Bio/SeqIO/fasta.pm ${P5SITE}/Bio/SeqIO/fastq.pm +${P5SITE}/Bio/SeqIO/flybase_chadoxml.pm ${P5SITE}/Bio/SeqIO/game/ ${P5SITE}/Bio/SeqIO/game.pm ${P5SITE}/Bio/SeqIO/game/featHandler.pm @@ -733,11 +802,13 @@ ${P5SITE}/Bio/SeqIO/game/gameHandler.pm ${P5SITE}/Bio/SeqIO/game/gameSubs.pm ${P5SITE}/Bio/SeqIO/game/gameWriter.pm ${P5SITE}/Bio/SeqIO/game/seqHandler.pm +${P5SITE}/Bio/SeqIO/gbdriver.pm ${P5SITE}/Bio/SeqIO/gcg.pm ${P5SITE}/Bio/SeqIO/genbank.pm ${P5SITE}/Bio/SeqIO/interpro.pm ${P5SITE}/Bio/SeqIO/kegg.pm ${P5SITE}/Bio/SeqIO/largefasta.pm +${P5SITE}/Bio/SeqIO/lasergene.pm ${P5SITE}/Bio/SeqIO/locuslink.pm ${P5SITE}/Bio/SeqIO/metafasta.pm ${P5SITE}/Bio/SeqIO/phd.pm @@ -746,8 +817,11 @@ ${P5SITE}/Bio/SeqIO/pln.pm ${P5SITE}/Bio/SeqIO/qual.pm ${P5SITE}/Bio/SeqIO/raw.pm ${P5SITE}/Bio/SeqIO/scf.pm +${P5SITE}/Bio/SeqIO/strider.pm ${P5SITE}/Bio/SeqIO/swiss.pm +${P5SITE}/Bio/SeqIO/swissdriver.pm ${P5SITE}/Bio/SeqIO/tab.pm +${P5SITE}/Bio/SeqIO/table.pm ${P5SITE}/Bio/SeqIO/tigr.pm ${P5SITE}/Bio/SeqIO/tigrxml.pm ${P5SITE}/Bio/SeqIO/tinyseq/ @@ -778,9 +852,9 @@ ${P5SITE}/Bio/Symbol/Alphabet.pm ${P5SITE}/Bio/Symbol/AlphabetI.pm ${P5SITE}/Bio/Symbol/DNAAlphabet.pm ${P5SITE}/Bio/Symbol/ProteinAlphabet.pm -${P5SITE}/Bio/Symbol/README.Symbol ${P5SITE}/Bio/Symbol/Symbol.pm ${P5SITE}/Bio/Symbol/SymbolI.pm +${P5SITE}/Bio/Taxon.pm ${P5SITE}/Bio/Taxonomy/ ${P5SITE}/Bio/Taxonomy.pm ${P5SITE}/Bio/Taxonomy/FactoryI.pm @@ -806,20 +880,6 @@ ${P5SITE}/Bio/Tools/Analysis/Protein/Scansite.pm ${P5SITE}/Bio/Tools/Analysis/Protein/Sopma.pm ${P5SITE}/Bio/Tools/Analysis/SimpleAnalysisBase.pm ${P5SITE}/Bio/Tools/AnalysisResult.pm -${P5SITE}/Bio/Tools/BPbl2seq.pm -${P5SITE}/Bio/Tools/BPlite/ -${P5SITE}/Bio/Tools/BPlite.pm -${P5SITE}/Bio/Tools/BPlite/HSP.pm -${P5SITE}/Bio/Tools/BPlite/Iteration.pm -${P5SITE}/Bio/Tools/BPlite/Sbjct.pm -${P5SITE}/Bio/Tools/BPpsilite.pm -${P5SITE}/Bio/Tools/Blast/ -${P5SITE}/Bio/Tools/Blast.pm -${P5SITE}/Bio/Tools/Blast/CHANGES -${P5SITE}/Bio/Tools/Blast/HSP.pm -${P5SITE}/Bio/Tools/Blast/HTML.pm -${P5SITE}/Bio/Tools/Blast/README -${P5SITE}/Bio/Tools/Blast/Sbjct.pm ${P5SITE}/Bio/Tools/Blat.pm ${P5SITE}/Bio/Tools/CodonTable.pm ${P5SITE}/Bio/Tools/Coil.pm @@ -827,7 +887,31 @@ ${P5SITE}/Bio/Tools/ECnumber.pm ${P5SITE}/Bio/Tools/EMBOSS/ ${P5SITE}/Bio/Tools/EMBOSS/Palindrome.pm ${P5SITE}/Bio/Tools/EPCR.pm +${P5SITE}/Bio/Tools/ERPIN.pm ${P5SITE}/Bio/Tools/ESTScan.pm +${P5SITE}/Bio/Tools/EUtilities/ +${P5SITE}/Bio/Tools/EUtilities.pm +${P5SITE}/Bio/Tools/EUtilities/Cookie.pm +${P5SITE}/Bio/Tools/EUtilities/EUtilDataI.pm +${P5SITE}/Bio/Tools/EUtilities/EUtilParameters.pm +${P5SITE}/Bio/Tools/EUtilities/History.pm +${P5SITE}/Bio/Tools/EUtilities/HistoryI.pm +${P5SITE}/Bio/Tools/EUtilities/Info/ +${P5SITE}/Bio/Tools/EUtilities/Info.pm +${P5SITE}/Bio/Tools/EUtilities/Info/FieldInfo.pm +${P5SITE}/Bio/Tools/EUtilities/Info/LinkInfo.pm +${P5SITE}/Bio/Tools/EUtilities/Link/ +${P5SITE}/Bio/Tools/EUtilities/Link.pm +${P5SITE}/Bio/Tools/EUtilities/Link/LinkSet.pm +${P5SITE}/Bio/Tools/EUtilities/Link/UrlLink.pm +${P5SITE}/Bio/Tools/EUtilities/Query/ +${P5SITE}/Bio/Tools/EUtilities/Query.pm +${P5SITE}/Bio/Tools/EUtilities/Query/GlobalQuery.pm +${P5SITE}/Bio/Tools/EUtilities/Summary/ +${P5SITE}/Bio/Tools/EUtilities/Summary.pm +${P5SITE}/Bio/Tools/EUtilities/Summary/DocSum.pm +${P5SITE}/Bio/Tools/EUtilities/Summary/Item.pm +${P5SITE}/Bio/Tools/EUtilities/Summary/ItemContainerI.pm ${P5SITE}/Bio/Tools/Eponine.pm ${P5SITE}/Bio/Tools/Est2Genome.pm ${P5SITE}/Bio/Tools/Fgenesh.pm @@ -848,10 +932,14 @@ ${P5SITE}/Bio/Tools/HMMER/Results.pm ${P5SITE}/Bio/Tools/HMMER/Set.pm ${P5SITE}/Bio/Tools/Hmmpfam.pm ${P5SITE}/Bio/Tools/IUPAC.pm +${P5SITE}/Bio/Tools/Infernal.pm ${P5SITE}/Bio/Tools/Lucy.pm ${P5SITE}/Bio/Tools/MZEF.pm +${P5SITE}/Bio/Tools/Match.pm ${P5SITE}/Bio/Tools/OddCodes.pm ${P5SITE}/Bio/Tools/Phylo/ +${P5SITE}/Bio/Tools/Phylo/Gerp.pm +${P5SITE}/Bio/Tools/Phylo/Gumby.pm ${P5SITE}/Bio/Tools/Phylo/Molphy/ ${P5SITE}/Bio/Tools/Phylo/Molphy.pm ${P5SITE}/Bio/Tools/Phylo/Molphy/Result.pm @@ -875,21 +963,24 @@ ${P5SITE}/Bio/Tools/Prints.pm ${P5SITE}/Bio/Tools/Profile.pm ${P5SITE}/Bio/Tools/Promoterwise.pm ${P5SITE}/Bio/Tools/PrositeScan.pm +${P5SITE}/Bio/Tools/Protparam.pm ${P5SITE}/Bio/Tools/Pseudowise.pm ${P5SITE}/Bio/Tools/QRNA.pm +${P5SITE}/Bio/Tools/RNAMotif.pm ${P5SITE}/Bio/Tools/RandomDistFunctions.pm ${P5SITE}/Bio/Tools/RepeatMasker.pm -${P5SITE}/Bio/Tools/RestrictionEnzyme.pm ${P5SITE}/Bio/Tools/Run/ ${P5SITE}/Bio/Tools/Run/GenericParameters.pm ${P5SITE}/Bio/Tools/Run/ParametersI.pm -${P5SITE}/Bio/Tools/Run/README ${P5SITE}/Bio/Tools/Run/RemoteBlast.pm ${P5SITE}/Bio/Tools/Run/StandAloneBlast.pm +${P5SITE}/Bio/Tools/Run/StandAloneNCBIBlast.pm +${P5SITE}/Bio/Tools/Run/StandAloneWUBlast.pm ${P5SITE}/Bio/Tools/Run/WrapperBase.pm ${P5SITE}/Bio/Tools/Seg.pm -${P5SITE}/Bio/Tools/SeqAnal.pm +${P5SITE}/Bio/Tools/SeqPattern/ ${P5SITE}/Bio/Tools/SeqPattern.pm +${P5SITE}/Bio/Tools/SeqPattern/Backtranslate.pm ${P5SITE}/Bio/Tools/SeqStats.pm ${P5SITE}/Bio/Tools/SeqWords.pm ${P5SITE}/Bio/Tools/SiRNA/ @@ -898,24 +989,31 @@ ${P5SITE}/Bio/Tools/SiRNA/Ruleset/ ${P5SITE}/Bio/Tools/SiRNA/Ruleset/saigo.pm ${P5SITE}/Bio/Tools/SiRNA/Ruleset/tuschl.pm ${P5SITE}/Bio/Tools/Sigcleave.pm +${P5SITE}/Bio/Tools/Signalp/ ${P5SITE}/Bio/Tools/Signalp.pm +${P5SITE}/Bio/Tools/Signalp/ExtendedSignalp.pm ${P5SITE}/Bio/Tools/Sim4/ ${P5SITE}/Bio/Tools/Sim4/Exon.pm ${P5SITE}/Bio/Tools/Sim4/Results.pm ${P5SITE}/Bio/Tools/Spidey/ ${P5SITE}/Bio/Tools/Spidey/Exon.pm ${P5SITE}/Bio/Tools/Spidey/Results.pm +${P5SITE}/Bio/Tools/TandemRepeatsFinder.pm +${P5SITE}/Bio/Tools/TargetP.pm ${P5SITE}/Bio/Tools/Tmhmm.pm -${P5SITE}/Bio/Tools/WWW.pm -${P5SITE}/Bio/Tools/WebBlat.pm ${P5SITE}/Bio/Tools/dpAlign.pm +${P5SITE}/Bio/Tools/ipcress.pm +${P5SITE}/Bio/Tools/isPcr.pm ${P5SITE}/Bio/Tools/pICalculator.pm ${P5SITE}/Bio/Tools/pSW.pm ${P5SITE}/Bio/Tools/tRNAscanSE.pm ${P5SITE}/Bio/Tree/ ${P5SITE}/Bio/Tree/AlleleNode.pm -${P5SITE}/Bio/Tree/Cladogram.pm +${P5SITE}/Bio/Tree/AnnotatableNode.pm +${P5SITE}/Bio/Tree/Compatible.pm ${P5SITE}/Bio/Tree/DistanceFactory.pm +${P5SITE}/Bio/Tree/Draw/ +${P5SITE}/Bio/Tree/Draw/Cladogram.pm ${P5SITE}/Bio/Tree/Node.pm ${P5SITE}/Bio/Tree/NodeI.pm ${P5SITE}/Bio/Tree/NodeNHX.pm @@ -933,6 +1031,7 @@ ${P5SITE}/Bio/TreeIO/newick.pm ${P5SITE}/Bio/TreeIO/nexus.pm ${P5SITE}/Bio/TreeIO/nhx.pm ${P5SITE}/Bio/TreeIO/pag.pm +${P5SITE}/Bio/TreeIO/phyloxml.pm ${P5SITE}/Bio/TreeIO/svggraph.pm ${P5SITE}/Bio/TreeIO/tabtree.pm ${P5SITE}/Bio/UpdateableSeqI.pm @@ -945,17 +1044,930 @@ ${P5SITE}/Bio/Variation/IO/ ${P5SITE}/Bio/Variation/IO.pm ${P5SITE}/Bio/Variation/IO/flat.pm ${P5SITE}/Bio/Variation/IO/xml.pm -${P5SITE}/Bio/Variation/README ${P5SITE}/Bio/Variation/RNAChange.pm ${P5SITE}/Bio/Variation/SNP.pm ${P5SITE}/Bio/Variation/SeqDiff.pm ${P5SITE}/Bio/Variation/VariantI.pm ${P5SITE}/Bio/WebAgent.pm -${P5SITE}/biodatabases.pod -${P5SITE}/biodesign.pod -${P5SITE}/bioperl.pod -${P5SITE}/bioscripts.pod -${P5SITE}/bptutorial.pl +@man man/man1/bp_aacomp.pl.1 +@man man/man1/bp_biblio.pl.1 +@man man/man1/bp_biofetch_genbank_proxy.pl.1 +@man man/man1/bp_bioflat_index.pl.1 +@man man/man1/bp_biogetseq.pl.1 +@man man/man1/bp_blast2tree.pl.1 +@man man/man1/bp_bulk_load_gff.pl.1 +@man man/man1/bp_chaos_plot.pl.1 +@man man/man1/bp_classify_hits_kingdom.pl.1 +@man man/man1/bp_composite_LD.pl.1 +@man man/man1/bp_dbsplit.pl.1 +@man man/man1/bp_download_query_genbank.pl.1 +@man man/man1/bp_einfo.pl.1 +@man man/man1/bp_extract_feature_seq.pl.1 +@man man/man1/bp_fast_load_gff.pl.1 +@man man/man1/bp_fastam9_to_table.pl.1 +@man man/man1/bp_fetch.pl.1 +@man man/man1/bp_filter_search.pl.1 +@man man/man1/bp_flanks.pl.1 +@man man/man1/bp_gccalc.pl.1 +@man man/man1/bp_genbank2gff.pl.1 +@man man/man1/bp_genbank2gff3.pl.1 +@man man/man1/bp_generate_histogram.pl.1 +@man man/man1/bp_heterogeneity_test.pl.1 +@man man/man1/bp_hivq.pl.1 +@man man/man1/bp_hmmer_to_table.pl.1 +@man man/man1/bp_index.pl.1 +@man man/man1/bp_load_gff.pl.1 +@man man/man1/bp_local_taxonomydb_query.pl.1 +@man man/man1/bp_make_mrna_protein.pl.1 +@man man/man1/bp_mask_by_search.pl.1 +@man man/man1/bp_meta_gff.pl.1 +@man man/man1/bp_mrtrans.pl.1 +@man man/man1/bp_mutate.pl.1 +@man man/man1/bp_nexus2nh.pl.1 +@man man/man1/bp_nrdb.pl.1 +@man man/man1/bp_oligo_count.pl.1 +@man man/man1/bp_pairwise_kaks.pl.1 +@man man/man1/bp_parse_hmmsearch.pl.1 +@man man/man1/bp_process_gadfly.pl.1 +@man man/man1/bp_process_sgd.pl.1 +@man man/man1/bp_process_wormbase.pl.1 +@man man/man1/bp_query_entrez_taxa.pl.1 +@man man/man1/bp_remote_blast.pl.1 +@man man/man1/bp_revtrans-motif.pl.1 +@man man/man1/bp_search2BSML.pl.1 +@man man/man1/bp_search2alnblocks.pl.1 +@man man/man1/bp_search2gff.pl.1 +@man man/man1/bp_search2table.pl.1 +@man man/man1/bp_search2tribe.pl.1 +@man man/man1/bp_seq_length.pl.1 +@man man/man1/bp_seqconvert.pl.1 +@man man/man1/bp_seqret.pl.1 +@man man/man1/bp_seqretsplit.pl.1 +@man man/man1/bp_split_seq.pl.1 +@man man/man1/bp_sreformat.pl.1 +@man man/man1/bp_taxid4species.pl.1 +@man man/man1/bp_taxonomy2tree.pl.1 +@man man/man1/bp_translate_seq.pl.1 +@man man/man1/bp_tree2pag.pl.1 +@man man/man1/bp_unflatten_seq.pl.1 +@man man/man3p/Bio::Align::AlignI.3p +@man man/man3p/Bio::Align::DNAStatistics.3p +@man man/man3p/Bio::Align::PairwiseStatistics.3p +@man man/man3p/Bio::Align::ProteinStatistics.3p +@man man/man3p/Bio::Align::StatisticsI.3p +@man man/man3p/Bio::Align::Utilities.3p +@man man/man3p/Bio::AlignIO.3p +@man man/man3p/Bio::AlignIO::Handler::GenericAlignHandler.3p +@man man/man3p/Bio::AlignIO::arp.3p +@man man/man3p/Bio::AlignIO::bl2seq.3p +@man man/man3p/Bio::AlignIO::clustalw.3p +@man man/man3p/Bio::AlignIO::emboss.3p +@man man/man3p/Bio::AlignIO::fasta.3p +@man man/man3p/Bio::AlignIO::largemultifasta.3p +@man man/man3p/Bio::AlignIO::maf.3p +@man man/man3p/Bio::AlignIO::mase.3p +@man man/man3p/Bio::AlignIO::mega.3p +@man man/man3p/Bio::AlignIO::meme.3p +@man man/man3p/Bio::AlignIO::metafasta.3p +@man man/man3p/Bio::AlignIO::msf.3p +@man man/man3p/Bio::AlignIO::nexus.3p +@man man/man3p/Bio::AlignIO::pfam.3p +@man man/man3p/Bio::AlignIO::phylip.3p +@man man/man3p/Bio::AlignIO::po.3p +@man man/man3p/Bio::AlignIO::proda.3p +@man man/man3p/Bio::AlignIO::prodom.3p +@man man/man3p/Bio::AlignIO::psi.3p +@man man/man3p/Bio::AlignIO::selex.3p +@man man/man3p/Bio::AlignIO::stockholm.3p +@man man/man3p/Bio::AlignIO::xmfa.3p +@man man/man3p/Bio::AnalysisI.3p +@man man/man3p/Bio::AnalysisParserI.3p +@man man/man3p/Bio::AnalysisResultI.3p +@man man/man3p/Bio::AnnotatableI.3p +@man man/man3p/Bio::Annotation::AnnotationFactory.3p +@man man/man3p/Bio::Annotation::Collection.3p +@man man/man3p/Bio::Annotation::Comment.3p +@man man/man3p/Bio::Annotation::DBLink.3p +@man man/man3p/Bio::Annotation::OntologyTerm.3p +@man man/man3p/Bio::Annotation::Reference.3p +@man man/man3p/Bio::Annotation::Relation.3p +@man man/man3p/Bio::Annotation::SimpleValue.3p +@man man/man3p/Bio::Annotation::StructuredValue.3p +@man man/man3p/Bio::Annotation::TagTree.3p +@man man/man3p/Bio::Annotation::Target.3p +@man man/man3p/Bio::Annotation::Tree.3p +@man man/man3p/Bio::Annotation::TypeManager.3p +@man man/man3p/Bio::AnnotationCollectionI.3p +@man man/man3p/Bio::AnnotationI.3p +@man man/man3p/Bio::Assembly::Contig.3p +@man man/man3p/Bio::Assembly::ContigAnalysis.3p +@man man/man3p/Bio::Assembly::IO.3p +@man man/man3p/Bio::Assembly::IO::ace.3p +@man man/man3p/Bio::Assembly::IO::phrap.3p +@man man/man3p/Bio::Assembly::IO::tigr.3p +@man man/man3p/Bio::Assembly::Scaffold.3p +@man man/man3p/Bio::Assembly::ScaffoldI.3p +@man man/man3p/Bio::Assembly::Singlet.3p +@man man/man3p/Bio::Assembly::Tools::ContigSpectrum.3p +@man man/man3p/Bio::Biblio.3p +@man man/man3p/Bio::Biblio::Article.3p +@man man/man3p/Bio::Biblio::BiblioBase.3p +@man man/man3p/Bio::Biblio::Book.3p +@man man/man3p/Bio::Biblio::BookArticle.3p +@man man/man3p/Bio::Biblio::IO.3p +@man man/man3p/Bio::Biblio::IO::medline2ref.3p +@man man/man3p/Bio::Biblio::IO::medlinexml.3p +@man man/man3p/Bio::Biblio::IO::pubmed2ref.3p +@man man/man3p/Bio::Biblio::IO::pubmedxml.3p +@man man/man3p/Bio::Biblio::Journal.3p +@man man/man3p/Bio::Biblio::JournalArticle.3p +@man man/man3p/Bio::Biblio::MedlineArticle.3p +@man man/man3p/Bio::Biblio::MedlineBook.3p +@man man/man3p/Bio::Biblio::MedlineBookArticle.3p +@man man/man3p/Bio::Biblio::MedlineJournal.3p +@man man/man3p/Bio::Biblio::MedlineJournalArticle.3p +@man man/man3p/Bio::Biblio::Organisation.3p +@man man/man3p/Bio::Biblio::Patent.3p +@man man/man3p/Bio::Biblio::Person.3p +@man man/man3p/Bio::Biblio::Proceeding.3p +@man man/man3p/Bio::Biblio::Provider.3p +@man man/man3p/Bio::Biblio::PubmedArticle.3p +@man man/man3p/Bio::Biblio::PubmedBookArticle.3p +@man man/man3p/Bio::Biblio::PubmedJournalArticle.3p +@man man/man3p/Bio::Biblio::Ref.3p +@man man/man3p/Bio::Biblio::Service.3p +@man man/man3p/Bio::Biblio::TechReport.3p +@man man/man3p/Bio::Biblio::Thesis.3p +@man man/man3p/Bio::Biblio::WebResource.3p +@man man/man3p/Bio::Cluster::ClusterFactory.3p +@man man/man3p/Bio::Cluster::FamilyI.3p +@man man/man3p/Bio::Cluster::SequenceFamily.3p +@man man/man3p/Bio::Cluster::UniGene.3p +@man man/man3p/Bio::Cluster::UniGeneI.3p +@man man/man3p/Bio::ClusterI.3p +@man man/man3p/Bio::ClusterIO.3p +@man man/man3p/Bio::ClusterIO::dbsnp.3p +@man man/man3p/Bio::ClusterIO::unigene.3p +@man 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man/man3p/Bio::TreeIO::phyloxml.3p +@man man/man3p/Bio::TreeIO::svggraph.3p +@man man/man3p/Bio::TreeIO::tabtree.3p +@man man/man3p/Bio::UpdateableSeqI.3p +@man man/man3p/Bio::Variation::AAChange.3p +@man man/man3p/Bio::Variation::AAReverseMutate.3p +@man man/man3p/Bio::Variation::Allele.3p +@man man/man3p/Bio::Variation::DNAMutation.3p +@man man/man3p/Bio::Variation::IO.3p +@man man/man3p/Bio::Variation::IO::flat.3p +@man man/man3p/Bio::Variation::IO::xml.3p +@man man/man3p/Bio::Variation::RNAChange.3p +@man man/man3p/Bio::Variation::SNP.3p +@man man/man3p/Bio::Variation::SeqDiff.3p +@man man/man3p/Bio::Variation::VariantI.3p +@man man/man3p/Bio::WebAgent.3p share/examples/bioperl/ share/examples/bioperl/Bio-DB-GFF/ share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl @@ -965,15 +1977,9 @@ share/examples/bioperl/align/aligntutorial.pl share/examples/bioperl/align/clustalw.pl share/examples/bioperl/align/simplealign.pl share/examples/bioperl/biblio/ -share/examples/bioperl/biblio/biblio_examples.pl +share/examples/bioperl/biblio/biblio-eutils-example.pl +share/examples/bioperl/biblio/biblio-soap-example.pl share/examples/bioperl/biblio/biblio_soap.pl -share/examples/bioperl/biographics/ -share/examples/bioperl/biographics/all_glyphs.pl -share/examples/bioperl/biographics/dynamic_glyphs.pl -share/examples/bioperl/biographics/feature_data.gff -share/examples/bioperl/biographics/feature_data.txt -share/examples/bioperl/biographics/lots_of_glyphs.pl -share/examples/bioperl/biographics/render_sequence.pl share/examples/bioperl/bioperl.pl share/examples/bioperl/cluster/ share/examples/bioperl/cluster/dbsnp.pl @@ -993,10 +1999,11 @@ share/examples/bioperl/generate_random_seq.pl share/examples/bioperl/liveseq/ share/examples/bioperl/liveseq/change_gene.pl share/examples/bioperl/longorf.pl -share/examples/bioperl/make_mrna_protein.pl share/examples/bioperl/make_primers.pl share/examples/bioperl/popgen/ share/examples/bioperl/popgen/parse_calc_stats.pl +share/examples/bioperl/quality/ +share/examples/bioperl/quality/svgtrace.pl share/examples/bioperl/rev_and_trans.pl share/examples/bioperl/revcom_dir.pl share/examples/bioperl/root/ @@ -1011,7 +2018,6 @@ share/examples/bioperl/root/lib/Bio/PrimarySeq.pm share/examples/bioperl/root/lib/Bio/PrimarySeqI.pm share/examples/bioperl/root/lib/Bio/Seq.pm share/examples/bioperl/root/lib/Bio/SeqI.pm -share/examples/bioperl/root/lib/Error.pm share/examples/bioperl/root/lib/TestInterface.pm share/examples/bioperl/root/lib/TestObject.pm share/examples/bioperl/searchio/ @@ -1036,11 +2042,14 @@ share/examples/bioperl/tk/ share/examples/bioperl/tk/gsequence.pl share/examples/bioperl/tk/hitdisplay.pl share/examples/bioperl/tools/ +share/examples/bioperl/tools/extract_genes.pl share/examples/bioperl/tools/gb_to_gff.pl share/examples/bioperl/tools/gff2ps.pl share/examples/bioperl/tools/parse_codeml.pl share/examples/bioperl/tools/psw.pl +share/examples/bioperl/tools/reverse-translate.pl share/examples/bioperl/tools/run_genscan.pl +share/examples/bioperl/tools/run_primer3.pl share/examples/bioperl/tools/seq_pattern.pl share/examples/bioperl/tools/standaloneblast.pl share/examples/bioperl/tree/