5 files changed, 976 insertions, 984 deletions

diff --git a/biology/p5-Bio-Graphics/pkg-plist b/biology/p5-Bio-Graphics/pkg-plist
index b97abc1acadf..c84139e3fef7 100644
--- a/biology/p5-Bio-Graphics/pkg-plist
+++ b/biology/p5-Bio-Graphics/pkg-plist
@@ -4,106 +4,6 @@ bin/frend.pl
 bin/glyph_help.pl
 bin/render_msa.pl
 bin/search_overview.pl
-%%PERL5_MAN3%%/Bio::Graphics.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::ConfiguratorI.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::DrawTransmembrane.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Feature.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::FeatureBase.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::FeatureDir.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::FeatureFile.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::FeatureFile::Iterator.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::Factory.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::alignment.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::allele_tower.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::anchored_arrow.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::arrow.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::box.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::broken_line.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::cds.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::christmas_arrow.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::crossbox.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::dashed_line.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::decorated_gene.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::decorated_transcript.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::diamond.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::dna.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::dot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::dumbbell.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::ellipse.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::ex.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::extending_arrow.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::fb_shmiggle.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::fixedwidth.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::flag.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::gene.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::generic.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::graded_segments.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::group.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::hat.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::heat_map.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::heat_map_ideogram.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::heterogeneous_segments.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::hidden.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::hybrid_plot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::ideogram.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::image.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::lightning.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::line.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::merge_parts.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::merged_alignment.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::minmax.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::operon.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::oval.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::pairplot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::pentagram.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::phylo_align.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::pinsertion.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::primers.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::processed_transcript.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::protein.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::ragged_ends.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::rainbow_gene.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::redgreen_box.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::redgreen_segment.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::repeating_shape.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::rndrect.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::ruler_arrow.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::saw_teeth.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::scale.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::segmented_keyglyph.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::segments.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::so_transcript.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::span.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::spectrogram.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::splice_site.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::stackedplot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::ternary_plot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::text_in_box.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::three_letters.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::tic_tac_toe.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::toomany.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::trace.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::track.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::transcript.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::transcript2.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::translation.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::triangle.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::two_bolts.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::vista_plot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::wave.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::weighted_arrow.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::whiskerplot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_box.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_density.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_xyplot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Glyph::xyplot.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Panel.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Pictogram.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::RendererI.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Util.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Wiggle.3.gz
-%%PERL5_MAN3%%/Bio::Graphics::Wiggle::Loader.3.gz
 %%SITE_PERL%%/Bio/Graphics.pm
 %%SITE_PERL%%/Bio/Graphics/ConfiguratorI.pm
 %%SITE_PERL%%/Bio/Graphics/DrawTransmembrane.pm
@@ -212,6 +112,106 @@ bin/search_overview.pl
 %%SITE_PERL%%/Bio/Graphics/Util.pm
 %%SITE_PERL%%/Bio/Graphics/Wiggle.pm
 %%SITE_PERL%%/Bio/Graphics/Wiggle/Loader.pm
+%%PERL5_MAN3%%/Bio::Graphics.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::ConfiguratorI.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::DrawTransmembrane.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Feature.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureBase.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureDir.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureFile.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureFile::Iterator.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::Factory.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::alignment.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::allele_tower.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::anchored_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::broken_line.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::cds.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::christmas_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::crossbox.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dashed_line.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::decorated_gene.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::decorated_transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::diamond.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dna.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dumbbell.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ellipse.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ex.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::extending_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::fb_shmiggle.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::fixedwidth.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::flag.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::gene.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::generic.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::graded_segments.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::group.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::hat.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::heat_map.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::heat_map_ideogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::heterogeneous_segments.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::hidden.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::hybrid_plot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ideogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::image.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::lightning.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::line.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::merge_parts.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::merged_alignment.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::minmax.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::operon.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::oval.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::pairplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::pentagram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::phylo_align.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::pinsertion.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::primers.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::processed_transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::protein.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ragged_ends.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::rainbow_gene.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::redgreen_box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::redgreen_segment.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::repeating_shape.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::rndrect.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ruler_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::saw_teeth.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::scale.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::segmented_keyglyph.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::segments.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::so_transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::span.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::spectrogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::splice_site.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::stackedplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ternary_plot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::text_in_box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::three_letters.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::tic_tac_toe.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::toomany.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::trace.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::track.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::transcript2.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::translation.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::triangle.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::two_bolts.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::vista_plot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wave.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::weighted_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::whiskerplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_density.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_xyplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::xyplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Panel.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Pictogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::RendererI.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Util.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Wiggle.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Wiggle::Loader.3.gz
 man/man1/contig_draw.pl.1.gz
 man/man1/feature_draw.pl.1.gz
 man/man1/frend.pl.1.gz
diff --git a/biology/p5-Bio-MAGETAB/pkg-plist b/biology/p5-Bio-MAGETAB/pkg-plist
index 14895b84aeb0..2e4eb84bec37 100644
--- a/biology/p5-Bio-MAGETAB/pkg-plist
+++ b/biology/p5-Bio-MAGETAB/pkg-plist
@@ -5,59 +5,59 @@ bin/unload_magetab_namespace.pl
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm
-%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm
-%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/ADF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Writer/ADF.pm
-%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Writer/IDF.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Writer/SDRF.pm
-%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm
+%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Writer.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Builder.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/DBLoader.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/RewriteAE.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Persistence.pm
-%%SITE_PERL%%/Bio/MAGETAB/Material.pm
-%%SITE_PERL%%/Bio/MAGETAB/Types.pm
-%%SITE_PERL%%/Bio/MAGETAB/ControlledTerm.pm
-%%SITE_PERL%%/Bio/MAGETAB/Contact.pm
-%%SITE_PERL%%/Bio/MAGETAB/DesignElement.pm
-%%SITE_PERL%%/Bio/MAGETAB/Investigation.pm
+%%SITE_PERL%%/Bio/MAGETAB/ArrayDesign.pm
+%%SITE_PERL%%/Bio/MAGETAB/Assay.pm
+%%SITE_PERL%%/Bio/MAGETAB/BaseClass.pm
 %%SITE_PERL%%/Bio/MAGETAB/Comment.pm
-%%SITE_PERL%%/Bio/MAGETAB/Publication.pm
-%%SITE_PERL%%/Bio/MAGETAB/Sample.pm
+%%SITE_PERL%%/Bio/MAGETAB/CompositeElement.pm
+%%SITE_PERL%%/Bio/MAGETAB/Contact.pm
+%%SITE_PERL%%/Bio/MAGETAB/ControlledTerm.pm
+%%SITE_PERL%%/Bio/MAGETAB/DataAcquisition.pm
 %%SITE_PERL%%/Bio/MAGETAB/DataFile.pm
-%%SITE_PERL%%/Bio/MAGETAB/ArrayDesign.pm
-%%SITE_PERL%%/Bio/MAGETAB/Event.pm
+%%SITE_PERL%%/Bio/MAGETAB/DataMatrix.pm
+%%SITE_PERL%%/Bio/MAGETAB/DatabaseEntry.pm
+%%SITE_PERL%%/Bio/MAGETAB/Data.pm
+%%SITE_PERL%%/Bio/MAGETAB/DesignElement.pm
 %%SITE_PERL%%/Bio/MAGETAB/Edge.pm
+%%SITE_PERL%%/Bio/MAGETAB/Event.pm
+%%SITE_PERL%%/Bio/MAGETAB/Extract.pm
+%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm
+%%SITE_PERL%%/Bio/MAGETAB/Factor.pm
+%%SITE_PERL%%/Bio/MAGETAB/Feature.pm
+%%SITE_PERL%%/Bio/MAGETAB/Investigation.pm
+%%SITE_PERL%%/Bio/MAGETAB/LabeledExtract.pm
+%%SITE_PERL%%/Bio/MAGETAB/Material.pm
 %%SITE_PERL%%/Bio/MAGETAB/MatrixColumn.pm
-%%SITE_PERL%%/Bio/MAGETAB/Normalization.pm
-%%SITE_PERL%%/Bio/MAGETAB/ParameterValue.pm
-%%SITE_PERL%%/Bio/MAGETAB/DataAcquisition.pm
-%%SITE_PERL%%/Bio/MAGETAB/Assay.pm
-%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm
-%%SITE_PERL%%/Bio/MAGETAB/SDRF.pm
-%%SITE_PERL%%/Bio/MAGETAB/Data.pm
 %%SITE_PERL%%/Bio/MAGETAB/MatrixRow.pm
-%%SITE_PERL%%/Bio/MAGETAB/Extract.pm
 %%SITE_PERL%%/Bio/MAGETAB/Measurement.pm
-%%SITE_PERL%%/Bio/MAGETAB/TermSource.pm
-%%SITE_PERL%%/Bio/MAGETAB/CompositeElement.pm
-%%SITE_PERL%%/Bio/MAGETAB/BaseClass.pm
 %%SITE_PERL%%/Bio/MAGETAB/Node.pm
+%%SITE_PERL%%/Bio/MAGETAB/Normalization.pm
+%%SITE_PERL%%/Bio/MAGETAB/ParameterValue.pm
+%%SITE_PERL%%/Bio/MAGETAB/ProtocolApplication.pm
+%%SITE_PERL%%/Bio/MAGETAB/ProtocolParameter.pm
 %%SITE_PERL%%/Bio/MAGETAB/Protocol.pm
+%%SITE_PERL%%/Bio/MAGETAB/Publication.pm
 %%SITE_PERL%%/Bio/MAGETAB/Reporter.pm
-%%SITE_PERL%%/Bio/MAGETAB/Factor.pm
-%%SITE_PERL%%/Bio/MAGETAB/ProtocolApplication.pm
-%%SITE_PERL%%/Bio/MAGETAB/LabeledExtract.pm
-%%SITE_PERL%%/Bio/MAGETAB/Feature.pm
-%%SITE_PERL%%/Bio/MAGETAB/DatabaseEntry.pm
+%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm
+%%SITE_PERL%%/Bio/MAGETAB/SDRF.pm
+%%SITE_PERL%%/Bio/MAGETAB/Sample.pm
 %%SITE_PERL%%/Bio/MAGETAB/Source.pm
-%%SITE_PERL%%/Bio/MAGETAB/ProtocolParameter.pm
-%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm
-%%SITE_PERL%%/Bio/MAGETAB/DataMatrix.pm
+%%SITE_PERL%%/Bio/MAGETAB/TermSource.pm
+%%SITE_PERL%%/Bio/MAGETAB/Types.pm
 %%SITE_PERL%%/Bio/MAGETAB.pm
 %%PERL5_MAN3%%/Bio::MAGETAB.3.gz
 %%PERL5_MAN3%%/Bio::MAGETAB::ArrayDesign.3.gz
diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index 2166c4ffb5e0..b4648d94440e 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -41,13 +41,13 @@ SHEBANG_FILES=	scripts/bioperl_application_installer.PLS \
 OPTIONS_DEFINE=	DOCS
 
 post-build:
-	cd ${WRKSRC} && ${PERL} ./Build manifest
+	(cd ${WRKSRC} && ${PERL} ./Build manifest)
 
 post-install:
 .for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
 	${CP} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
 .endfor
-	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 .for doc in AUTHORS Changes INSTALL.PROGRAMS README
 	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
 .endfor
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 6eda916ff372..3430fe8c7d1e 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	bioperl
 PORTVERSION=	1.6.924
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
@@ -16,51 +16,47 @@ COMMENT=	Collection of Perl modules for bioinformatics
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \
+BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \
+		p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \
 		p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
 		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \
+		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
+		p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \
 		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
-		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
-		p5-Data-Stag>=0:${PORTSDIR}/devel/p5-Data-Stag \
+		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
+		p5-Error>=0:${PORTSDIR}/lang/p5-Error \
+		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
 		p5-GD-SVG>=0:${PORTSDIR}/graphics/p5-GD-SVG \
 		p5-Graph>=0:${PORTSDIR}/math/p5-Graph \
-		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
+		p5-GraphViz>=0:${PORTSDIR}/graphics/p5-GraphViz \
+		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
+		p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \
 		p5-IO-stringy>=0:${PORTSDIR}/devel/p5-IO-stringy \
 		p5-IO-String>=0:${PORTSDIR}/devel/p5-IO-String \
-		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
+		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
+		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
 		p5-SOAP-Lite>=0:${PORTSDIR}/net/p5-SOAP-Lite \
+		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
+		p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \
+		p5-Spreadsheet-ParseExcel>=0:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
 		p5-SVG>=0:${PORTSDIR}/textproc/p5-SVG \
 		p5-SVG-Graph>=0:${PORTSDIR}/graphics/p5-SVG-Graph \
+		p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \
 		p5-Text-Shellwords>=0:${PORTSDIR}/textproc/p5-Text-Shellwords \
+		p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \
+		p5-URI>=0:${PORTSDIR}/net/p5-URI \
 		p5-XML-DOM>=0:${PORTSDIR}/textproc/p5-XML-DOM \
 		p5-XML-DOM-XPath>=0:${PORTSDIR}/textproc/p5-XML-DOM-XPath \
-		p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml \
-		p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \
+		p5-XML-LibXML>=0:${PORTSDIR}/textproc/p5-XML-LibXML \
+		p5-XML-Parser>=0:${PORTSDIR}/textproc/p5-XML-Parser \
 		p5-XML-SAX>=0:${PORTSDIR}/textproc/p5-XML-SAX \
 		p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \
+		p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \
 		p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \
 		p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \
-		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
-		p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \
-		p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
-		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
-		p5-HTML-Parser>=0:${PORTSDIR}/www/p5-HTML-Parser \
-		p5-XML-Parser>=0:${PORTSDIR}/textproc/p5-XML-Parser \
-		p5-Spreadsheet-ParseExcel>=0:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \
-		p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \
-		p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \
-		p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \
-		p5-GraphViz>=0:${PORTSDIR}/graphics/p5-GraphViz \
-		p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \
-		p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \
-		p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \
-		p5-URI>=0:${PORTSDIR}/net/p5-URI \
-		p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \
-		p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \
-		p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \
-		p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \
 		p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \
-		p5-Error>=0:${PORTSDIR}/lang/p5-Error
+		p5-libwww>=0:${PORTSDIR}/www/p5-libwww \
+		p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml
 
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
@@ -75,19 +71,15 @@ PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg
 SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
 SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite
 
-.include <bsd.port.options.mk>
-
 post-install:
-	${MKDIR} ${STAGEDIR}${DATADIR}
+	@${MKDIR} ${STAGEDIR}${DATADIR}
 	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR}
-	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
-.if ${PORT_OPTIONS:MDOCS}
-	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 .for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
 	${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
 .endfor
 	${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR}
-.endif
 
 .include <bsd.port.mk>
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index 1203eb08e68d..74533a2e94ce 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -64,820 +64,6 @@ bin/bp_taxonomy2tree.pl
 bin/bp_translate_seq.pl
 bin/bp_tree2pag.pl
 bin/bp_unflatten_seq.pl
-%%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
-%%PERL5_MAN3%%/Bio::Align::Utilities.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::Handler::GenericAlignHandler.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::arp.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::bl2seq.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::clustalw.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::emboss.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::fasta.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::largemultifasta.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::maf.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::mase.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::mega.3.gz
-%%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
-%%PERL5_MAN3%%/Bio::AlignIO::po.3.gz
-%%PERL5_MAN3%%/Bio::AlignIO::proda.3.gz
-%%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
-%%PERL5_MAN3%%/Bio::AnalysisResultI.3.gz
-%%PERL5_MAN3%%/Bio::AnnotatableI.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::AnnotationFactory.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::Collection.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::Comment.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::DBLink.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::OntologyTerm.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::Reference.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::Relation.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::SimpleValue.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::StructuredValue.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::TagTree.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::Target.3.gz
-%%PERL5_MAN3%%/Bio::Annotation::Tree.3.gz
-%%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::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
-%%PERL5_MAN3%%/Bio::DB::DBFetch.3.gz
-%%PERL5_MAN3%%/Bio::DB::EMBL.3.gz
-%%PERL5_MAN3%%/Bio::DB::EntrezGene.3.gz
-%%PERL5_MAN3%%/Bio::DB::Expression.3.gz
-%%PERL5_MAN3%%/Bio::DB::Expression::geo.3.gz
-%%PERL5_MAN3%%/Bio::DB::Failover.3.gz
-%%PERL5_MAN3%%/Bio::DB::Fasta.3.gz
-%%PERL5_MAN3%%/Bio::DB::FileCache.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat::BDB.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat::BDB::embl.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat::BDB::fasta.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat::BDB::genbank.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat::BDB::swiss.3.gz
-%%PERL5_MAN3%%/Bio::DB::Flat::BinarySearch.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::ace.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::berkeleydb.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::berkeleydb::iterator.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::biofetch.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::biofetch_oracle.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::caching_handle.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::iterator.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysql.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysqlace.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::mysqlopt.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::oracle.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::oracleace.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::pg.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::dbi::pg_fts.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::memory.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::memory::feature_serializer.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Adaptor::memory::iterator.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::alignment.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::clone.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::coding.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::gene.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::match.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::none.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::orf.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::processed_transcript.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::so_transcript.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::transcript.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_acembly.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_ensgene.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_genscan.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_refgene.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_sanger22.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_softberry.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_twinscan.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Aggregator::ucsc_unigene.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Featname.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Feature.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Homol.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::RelSegment.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Segment.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Typename.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Util::Binning.3.gz
-%%PERL5_MAN3%%/Bio::DB::GFF::Util::Rearrange.3.gz
-%%PERL5_MAN3%%/Bio::DB::GenBank.3.gz
-%%PERL5_MAN3%%/Bio::DB::GenPept.3.gz
-%%PERL5_MAN3%%/Bio::DB::GenericWebAgent.3.gz
-%%PERL5_MAN3%%/Bio::DB::HIV.3.gz
-%%PERL5_MAN3%%/Bio::DB::HIV::HIVAnnotProcessor.3.gz
-%%PERL5_MAN3%%/Bio::DB::HIV::HIVQueryHelper.3.gz
-%%PERL5_MAN3%%/Bio::DB::InMemoryCache.3.gz
-%%PERL5_MAN3%%/Bio::DB::IndexedBase.3.gz
-%%PERL5_MAN3%%/Bio::DB::LocationI.3.gz
-%%PERL5_MAN3%%/Bio::DB::MeSH.3.gz
-%%PERL5_MAN3%%/Bio::DB::NCBIHelper.3.gz
-%%PERL5_MAN3%%/Bio::DB::Qual.3.gz
-%%PERL5_MAN3%%/Bio::DB::Query::GenBank.3.gz
-%%PERL5_MAN3%%/Bio::DB::Query::HIVQuery.3.gz
-%%PERL5_MAN3%%/Bio::DB::Query::WebQuery.3.gz
-%%PERL5_MAN3%%/Bio::DB::QueryI.3.gz
-%%PERL5_MAN3%%/Bio::DB::RandomAccessI.3.gz
-%%PERL5_MAN3%%/Bio::DB::RefSeq.3.gz
-%%PERL5_MAN3%%/Bio::DB::ReferenceI.3.gz
-%%PERL5_MAN3%%/Bio::DB::Registry.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::NormalizedFeature.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::NormalizedFeatureI.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::NormalizedTableFeatureI.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Segment.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::Iterator.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::Pg.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::SQLite.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::DBI::mysql.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::FeatureFileLoader.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::GFF2Loader.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::GFF3Loader.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::LoadHelper.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::Loader.3.gz
-%%PERL5_MAN3%%/Bio::DB::SeqFeature::Store::bdb.3.gz
-%%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
-%%PERL5_MAN3%%/Bio::DB::SwissProt.3.gz
-%%PERL5_MAN3%%/Bio::DB::TFBS.3.gz
-%%PERL5_MAN3%%/Bio::DB::TFBS::transfac_pro.3.gz
-%%PERL5_MAN3%%/Bio::DB::Taxonomy.3.gz
-%%PERL5_MAN3%%/Bio::DB::Taxonomy::entrez.3.gz
-%%PERL5_MAN3%%/Bio::DB::Taxonomy::flatfile.3.gz
-%%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::Universal.3.gz
-%%PERL5_MAN3%%/Bio::DB::UpdateableSeqI.3.gz
-%%PERL5_MAN3%%/Bio::DB::WebDBSeqI.3.gz
-%%PERL5_MAN3%%/Bio::DBLinkContainerI.3.gz
-%%PERL5_MAN3%%/Bio::Das::FeatureTypeI.3.gz
-%%PERL5_MAN3%%/Bio::Das::SegmentI.3.gz
-%%PERL5_MAN3%%/Bio::DasI.3.gz
-%%PERL5_MAN3%%/Bio::DescribableI.3.gz
-%%PERL5_MAN3%%/Bio::Draw::Pictogram.3.gz
-%%PERL5_MAN3%%/Bio::Event::EventGeneratorI.3.gz
-%%PERL5_MAN3%%/Bio::Event::EventHandlerI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::AnalysisI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::ApplicationFactoryI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::DriverFactory.3.gz
-%%PERL5_MAN3%%/Bio::Factory::FTLocationFactory.3.gz
-%%PERL5_MAN3%%/Bio::Factory::LocationFactoryI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::MapFactoryI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::ObjectBuilderI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::ObjectFactory.3.gz
-%%PERL5_MAN3%%/Bio::Factory::ObjectFactoryI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::SeqAnalysisParserFactory.3.gz
-%%PERL5_MAN3%%/Bio::Factory::SeqAnalysisParserFactoryI.3.gz
-%%PERL5_MAN3%%/Bio::Factory::SequenceFactoryI.3.gz
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+%%PERL5_MAN3%%/Bio::Tools::Tmhmm.3.gz
+%%PERL5_MAN3%%/Bio::Tools::dpAlign.3.gz
+%%PERL5_MAN3%%/Bio::Tools::ipcress.3.gz
+%%PERL5_MAN3%%/Bio::Tools::isPcr.3.gz
+%%PERL5_MAN3%%/Bio::Tools::pICalculator.3.gz
+%%PERL5_MAN3%%/Bio::Tools::pSW.3.gz
+%%PERL5_MAN3%%/Bio::Tools::tRNAscanSE.3.gz
+%%PERL5_MAN3%%/Bio::Tree::AlleleNode.3.gz
+%%PERL5_MAN3%%/Bio::Tree::AnnotatableNode.3.gz
+%%PERL5_MAN3%%/Bio::Tree::Compatible.3.gz
+%%PERL5_MAN3%%/Bio::Tree::DistanceFactory.3.gz
+%%PERL5_MAN3%%/Bio::Tree::Draw::Cladogram.3.gz
+%%PERL5_MAN3%%/Bio::Tree::Node.3.gz
+%%PERL5_MAN3%%/Bio::Tree::NodeI.3.gz
+%%PERL5_MAN3%%/Bio::Tree::NodeNHX.3.gz
+%%PERL5_MAN3%%/Bio::Tree::RandomFactory.3.gz
+%%PERL5_MAN3%%/Bio::Tree::Statistics.3.gz
+%%PERL5_MAN3%%/Bio::Tree::Tree.3.gz
+%%PERL5_MAN3%%/Bio::Tree::TreeFunctionsI.3.gz
+%%PERL5_MAN3%%/Bio::Tree::TreeI.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::NewickParser.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::TreeEventBuilder.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::cluster.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::lintree.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::newick.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::nexml.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::nexus.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::nhx.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::pag.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::phyloxml.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::svggraph.3.gz
+%%PERL5_MAN3%%/Bio::TreeIO::tabtree.3.gz
+%%PERL5_MAN3%%/Bio::UpdateableSeqI.3.gz
+%%PERL5_MAN3%%/Bio::Variation::AAChange.3.gz
+%%PERL5_MAN3%%/Bio::Variation::AAReverseMutate.3.gz
+%%PERL5_MAN3%%/Bio::Variation::Allele.3.gz
+%%PERL5_MAN3%%/Bio::Variation::DNAMutation.3.gz
+%%PERL5_MAN3%%/Bio::Variation::IO.3.gz
+%%PERL5_MAN3%%/Bio::Variation::IO::flat.3.gz
+%%PERL5_MAN3%%/Bio::Variation::IO::xml.3.gz
+%%PERL5_MAN3%%/Bio::Variation::RNAChange.3.gz
+%%PERL5_MAN3%%/Bio::Variation::SNP.3.gz
+%%PERL5_MAN3%%/Bio::Variation::SeqDiff.3.gz
+%%PERL5_MAN3%%/Bio::Variation::VariantI.3.gz
+%%PERL5_MAN3%%/Bio::WebAgent.3.gz
 man/man1/bp_aacomp.pl.1.gz
 man/man1/bp_biofetch_genbank_proxy.pl.1.gz
 man/man1/bp_bioflat_index.pl.1.gz