Index: head/biology/p5-BioPerl-Run/Makefile
===================================================================
--- head/biology/p5-BioPerl-Run/Makefile	(revision 449926)
+++ head/biology/p5-BioPerl-Run/Makefile	(revision 449927)
@@ -1,53 +1,53 @@
 # Created by: Mauricio Herrera Cuadra <mauricio@arareko.net>
 # $FreeBSD$
 
 PORTNAME=	BioPerl-Run
-PORTVERSION=	1.007001
-PORTREVISION=	1
+PORTVERSION=	1.007002
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
 PKGNAMEPREFIX=	p5-
 
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Wrapper modules for common bioinformatics tools
 
 LICENSE=	ART10 GPLv1+
 LICENSE_COMB=	dual
 LICENSE_FILE_ART10=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
+		p5-Bio-FeatureIO>=0:biology/p5-Bio-FeatureIO \
 		p5-BioPerl>=1.007000:biology/p5-BioPerl \
 		p5-Config-Any>=0:devel/p5-Config-Any \
 		p5-File-Sort>=0:misc/p5-File-Sort \
 		p5-IO-String>=0:devel/p5-IO-String \
 		p5-IPC-Run>=0:devel/p5-IPC-Run \
 		p5-XML-Twig>=0:textproc/p5-XML-Twig
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 CONFLICTS=	p5-bioperl-run-1.[13579]*
 
 OPTIONS_DEFINE=	DOCS
 
 NO_ARCH=	yes
 USES=		perl5 shebangfix
 USE_PERL5=	modbuild
 SHEBANG_FILES=	scripts/*
 
 PORTDOCS=	*
 
 post-build:
 	(cd ${WRKSRC} && ${PERL} ./Build manifest)
 
 post-install:
 .for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
 .endfor
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 .for doc in AUTHORS Changes INSTALL.PROGRAMS README.md
 	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
 .endfor
 
 .include <bsd.port.mk>
Index: head/biology/p5-BioPerl-Run/distinfo
===================================================================
--- head/biology/p5-BioPerl-Run/distinfo	(revision 449926)
+++ head/biology/p5-BioPerl-Run/distinfo	(revision 449927)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1482241323
-SHA256 (BioPerl-Run-1.007001.tar.gz) = 55fd632ff24af9b3b1ecf655906cd34c0460a48cb45faabc72dd327ee5e1b0cc
-SIZE (BioPerl-Run-1.007001.tar.gz) = 14548613
+TIMESTAMP = 1505487295
+SHA256 (BioPerl-Run-1.007002.tar.gz) = 29806fc407183a936897d49d01d227877f52c946e3ed96c0675ed1ed14e1ce07
+SIZE (BioPerl-Run-1.007002.tar.gz) = 14493777
Index: head/biology/p5-BioPerl-Run/pkg-plist
===================================================================
--- head/biology/p5-BioPerl-Run/pkg-plist	(revision 449926)
+++ head/biology/p5-BioPerl-Run/pkg-plist	(revision 449927)
@@ -1,269 +1,251 @@
 bin/bp_bioperl_application_installer
 bin/bp_multi_hmmsearch
 bin/bp_panalysis
 bin/bp_papplmaker
 bin/bp_run_neighbor
 bin/bp_run_protdist
 %%SITE_PERL%%/Bio/DB/ESoap.pm
 %%SITE_PERL%%/Bio/DB/ESoap/WSDL.pm
 %%SITE_PERL%%/Bio/DB/SoapEUtilities.pm
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-%%SITE_PERL%%/Bio/Installer/PAML.pm
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 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
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-%%SITE_PERL%%/Bio/Tools/Run/Alignment/TCoffee.pm
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 %%SITE_PERL%%/Bio/Tools/Run/Ensembl.pm
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 %%SITE_PERL%%/Bio/Tools/Run/FootPrinter.pm
 %%SITE_PERL%%/Bio/Tools/Run/Genemark.pm
 %%SITE_PERL%%/Bio/Tools/Run/Genewise.pm
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 %%SITE_PERL%%/Bio/Tools/Run/Glimmer.pm
 %%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
 %%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
 %%SITE_PERL%%/Bio/Tools/Run/MCS.pm
 %%SITE_PERL%%/Bio/Tools/Run/Maq.pm
 %%SITE_PERL%%/Bio/Tools/Run/Maq/Config.pm
 %%SITE_PERL%%/Bio/Tools/Run/Match.pm
 %%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
 %%SITE_PERL%%/Bio/Tools/Run/Meme.pm
 %%SITE_PERL%%/Bio/Tools/Run/Minimo.pm
 %%SITE_PERL%%/Bio/Tools/Run/Newbler.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/FastTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/REL.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/LVB.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree/Best.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Baseml.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Codeml.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Evolver.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML/Yn00.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Base.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Consense.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/PhyloBase.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Raxml.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/SLR.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Semphy.pm
 %%SITE_PERL%%/Bio/Tools/Run/Primate.pm
 %%SITE_PERL%%/Bio/Tools/Run/Primer3.pm
 %%SITE_PERL%%/Bio/Tools/Run/Prints.pm
 %%SITE_PERL%%/Bio/Tools/Run/Profile.pm
 %%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm
 %%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm
 %%SITE_PERL%%/Bio/Tools/Run/RNAMotif.pm
 %%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm
 %%SITE_PERL%%/Bio/Tools/Run/Samtools.pm
 %%SITE_PERL%%/Bio/Tools/Run/Samtools/Config.pm
 %%SITE_PERL%%/Bio/Tools/Run/Seg.pm
 %%SITE_PERL%%/Bio/Tools/Run/Signalp.pm
 %%SITE_PERL%%/Bio/Tools/Run/Simprot.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlast.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneNCBIBlast.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneWUBlast.pm
 %%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm
 %%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
 %%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
 %%SITE_PERL%%/Bio/Tools/Run/Vista.pm
 %%SITE_PERL%%/Bio/Tools/Run/WrapperBase.pm
 %%SITE_PERL%%/Bio/Tools/Run/WrapperBase/CommandExts.pm
 %%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm
 %%PERL5_MAN3%%/Bio::DB::ESoap.3.gz
 %%PERL5_MAN3%%/Bio::DB::ESoap::WSDL.3.gz
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities.3.gz
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities::DocSumAdaptor.3.gz
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities::FetchAdaptor.3.gz
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 %%PERL5_MAN3%%/Bio::Factory::EMBOSS.3.gz
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 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Blat.3.gz
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