sync with trunkbranch-1-6run-1-6-1_001
commit4133c9a12e608102ec20537519934c531fe9c077
authorcjfields <cjfields@bioperl.org>
Wed, 30 Sep 2009 04:30:42 +0000 (30 04:30 -0000)
committercjfields <cjfields@bioperl.org>
Wed, 30 Sep 2009 04:30:42 +0000 (30 04:30 -0000)
treebf24a25deed7a68d1fdaee3ed5d60a7ae9c46ff9
parent3250289f102398d2f575e01266c7206c43e0b394
sync with trunk

svn path=/bioperl-run/branches/branch-1-6/; revision=16221
98 files changed:
Changes
lib/Bio/Factory/EMBOSS.pm
lib/Bio/Installer/Clustalw.pm
lib/Bio/Installer/EMBOSS.pm
lib/Bio/Installer/Generic.pm
lib/Bio/Installer/Hyphy.pm
lib/Bio/Installer/Muscle.pm
lib/Bio/Installer/PAML.pm
lib/Bio/Installer/Probcons.pm
lib/Bio/Installer/SLR.pm
lib/Bio/Installer/TCoffee.pm
lib/Bio/Tools/Run/Alignment/Amap.pm
lib/Bio/Tools/Run/Alignment/Blat.pm
lib/Bio/Tools/Run/Alignment/Clustalw.pm
lib/Bio/Tools/Run/Alignment/DBA.pm
lib/Bio/Tools/Run/Alignment/Exonerate.pm
lib/Bio/Tools/Run/Alignment/Kalign.pm
lib/Bio/Tools/Run/Alignment/Lagan.pm
lib/Bio/Tools/Run/Alignment/MAFFT.pm
lib/Bio/Tools/Run/Alignment/Muscle.pm
lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
lib/Bio/Tools/Run/Alignment/Probalign.pm
lib/Bio/Tools/Run/Alignment/Probcons.pm
lib/Bio/Tools/Run/Alignment/Proda.pm
lib/Bio/Tools/Run/Alignment/Sim4.pm
lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
lib/Bio/Tools/Run/Alignment/TCoffee.pm
lib/Bio/Tools/Run/Analysis.pm
lib/Bio/Tools/Run/Analysis/soap.pm
lib/Bio/Tools/Run/AnalysisFactory.pm
lib/Bio/Tools/Run/AnalysisFactory/soap.pm
lib/Bio/Tools/Run/Cap3.pm
lib/Bio/Tools/Run/Coil.pm
lib/Bio/Tools/Run/EMBOSSApplication.pm
lib/Bio/Tools/Run/EMBOSSacd.pm
lib/Bio/Tools/Run/ERPIN.pm
lib/Bio/Tools/Run/Ensembl.pm
lib/Bio/Tools/Run/Eponine.pm
lib/Bio/Tools/Run/FootPrinter.pm
lib/Bio/Tools/Run/Genemark.pm
lib/Bio/Tools/Run/Genewise.pm
lib/Bio/Tools/Run/Genscan.pm
lib/Bio/Tools/Run/Glimmer.pm
lib/Bio/Tools/Run/Hmmer.pm
lib/Bio/Tools/Run/Infernal.pm
lib/Bio/Tools/Run/MCS.pm
lib/Bio/Tools/Run/Match.pm
lib/Bio/Tools/Run/Mdust.pm
lib/Bio/Tools/Run/Meme.pm
lib/Bio/Tools/Run/Phrap.pm
lib/Bio/Tools/Run/Phylo/Gerp.pm
lib/Bio/Tools/Run/Phylo/Gumby.pm
lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
lib/Bio/Tools/Run/Phylo/LVB.pm
lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
lib/Bio/Tools/Run/Phylo/PhyloBase.pm
lib/Bio/Tools/Run/Phylo/Phyml.pm
lib/Bio/Tools/Run/Phylo/QuickTree.pm
lib/Bio/Tools/Run/Phylo/SLR.pm
lib/Bio/Tools/Run/Phylo/Semphy.pm
lib/Bio/Tools/Run/Primate.pm
lib/Bio/Tools/Run/Primer3.pm
lib/Bio/Tools/Run/Prints.pm
lib/Bio/Tools/Run/Profile.pm
lib/Bio/Tools/Run/Promoterwise.pm
lib/Bio/Tools/Run/Pseudowise.pm
lib/Bio/Tools/Run/RNAMotif.pm
lib/Bio/Tools/Run/RepeatMasker.pm
lib/Bio/Tools/Run/Seg.pm
lib/Bio/Tools/Run/Signalp.pm
lib/Bio/Tools/Run/Simprot.pm
lib/Bio/Tools/Run/TigrAssembler.pm
lib/Bio/Tools/Run/TribeMCL.pm
lib/Bio/Tools/Run/Vista.pm
lib/Bio/Tools/Run/tRNAscanSE.pm
t/Infernal.t
t/data/purine.added.fa [new file with mode: 0644]
t/gmap-run.t