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moved Bio into lib to make Module::Build installation more normal

svn path=/bioperl-run/trunk/; revision=15911
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1 parent b244653 commit daaa8a4404f58c471131051ae5e0f505b0ba37c1 @sendu sendu committed
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  1. 0 { → lib}/Bio/Factory/EMBOSS.pm
  2. 0 { → lib}/Bio/Installer/Clustalw.pm
  3. 0 { → lib}/Bio/Installer/EMBOSS.pm
  4. 0 { → lib}/Bio/Installer/Generic.pm
  5. 0 { → lib}/Bio/Installer/Hyphy.pm
  6. 0 { → lib}/Bio/Installer/Muscle.pm
  7. 0 { → lib}/Bio/Installer/PAML.pm
  8. 0 { → lib}/Bio/Installer/Probcons.pm
  9. 0 { → lib}/Bio/Installer/SLR.pm
  10. 0 { → lib}/Bio/Installer/TCoffee.pm
  11. 0 { → lib}/Bio/Tools/Run/Alignment/Amap.pm
  12. 0 { → lib}/Bio/Tools/Run/Alignment/Blat.pm
  13. 0 { → lib}/Bio/Tools/Run/Alignment/Clustalw.pm
  14. 0 { → lib}/Bio/Tools/Run/Alignment/DBA.pm
  15. 0 { → lib}/Bio/Tools/Run/Alignment/Exonerate.pm
  16. 0 { → lib}/Bio/Tools/Run/Alignment/Kalign.pm
  17. 0 { → lib}/Bio/Tools/Run/Alignment/Lagan.pm
  18. 0 { → lib}/Bio/Tools/Run/Alignment/MAFFT.pm
  19. 0 { → lib}/Bio/Tools/Run/Alignment/Muscle.pm
  20. 0 { → lib}/Bio/Tools/Run/Alignment/Pal2Nal.pm
  21. 0 { → lib}/Bio/Tools/Run/Alignment/Probalign.pm
  22. 0 { → lib}/Bio/Tools/Run/Alignment/Probcons.pm
  23. 0 { → lib}/Bio/Tools/Run/Alignment/Proda.pm
  24. 0 { → lib}/Bio/Tools/Run/Alignment/Sim4.pm
  25. 0 { → lib}/Bio/Tools/Run/Alignment/StandAloneFasta.pm
  26. 0 { → lib}/Bio/Tools/Run/Alignment/TCoffee.pm
  27. 0 { → lib}/Bio/Tools/Run/Analysis.pm
  28. 0 { → lib}/Bio/Tools/Run/Analysis/soap.pm
  29. 0 { → lib}/Bio/Tools/Run/AnalysisFactory.pm
  30. 0 { → lib}/Bio/Tools/Run/AnalysisFactory/soap.pm
  31. 0 { → lib}/Bio/Tools/Run/Cap3.pm
  32. 0 { → lib}/Bio/Tools/Run/Coil.pm
  33. 0 { → lib}/Bio/Tools/Run/EMBOSSApplication.pm
  34. 0 { → lib}/Bio/Tools/Run/EMBOSSacd.pm
  35. 0 { → lib}/Bio/Tools/Run/ERPIN.pm
  36. 0 { → lib}/Bio/Tools/Run/Ensembl.pm
  37. 0 { → lib}/Bio/Tools/Run/Eponine.pm
  38. 0 { → lib}/Bio/Tools/Run/FootPrinter.pm
  39. 0 { → lib}/Bio/Tools/Run/Genemark.pm
  40. 0 { → lib}/Bio/Tools/Run/Genewise.pm
  41. 0 { → lib}/Bio/Tools/Run/Genscan.pm
  42. 0 { → lib}/Bio/Tools/Run/Glimmer.pm
  43. 0 { → lib}/Bio/Tools/Run/Hmmer.pm
  44. 0 { → lib}/Bio/Tools/Run/Infernal.pm
  45. 0 { → lib}/Bio/Tools/Run/MCS.pm
  46. 0 { → lib}/Bio/Tools/Run/Match.pm
  47. 0 { → lib}/Bio/Tools/Run/Mdust.pm
  48. 0 { → lib}/Bio/Tools/Run/Meme.pm
  49. 0 { → lib}/Bio/Tools/Run/Phrap.pm
  50. 0 { → lib}/Bio/Tools/Run/Phylo/Gerp.pm
  51. 0 { → lib}/Bio/Tools/Run/Phylo/Gumby.pm
  52. 0 { → lib}/Bio/Tools/Run/Phylo/Hyphy/Base.pm
  53. 0 { → lib}/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
  54. 0 { → lib}/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
  55. 0 { → lib}/Bio/Tools/Run/Phylo/Hyphy/REL.pm
  56. 0 { → lib}/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
  57. 0 { → lib}/Bio/Tools/Run/Phylo/LVB.pm
  58. 0 { → lib}/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
  59. 0 { → lib}/Bio/Tools/Run/Phylo/Njtree/Best.pm
  60. 0 { → lib}/Bio/Tools/Run/Phylo/PAML/Baseml.pm
  61. 0 { → lib}/Bio/Tools/Run/Phylo/PAML/Codeml.pm
  62. 0 { → lib}/Bio/Tools/Run/Phylo/PAML/Evolver.pm
  63. 0 { → lib}/Bio/Tools/Run/Phylo/PAML/Yn00.pm
  64. 0 { → lib}/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
  65. 0 { → lib}/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
  66. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/Base.pm
  67. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/Consense.pm
  68. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
  69. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
  70. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
  71. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
  72. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
  73. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
  74. 0 { → lib}/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
  75. 0 { → lib}/Bio/Tools/Run/Phylo/PhyloBase.pm
  76. 0 { → lib}/Bio/Tools/Run/Phylo/Phyml.pm
  77. 0 { → lib}/Bio/Tools/Run/Phylo/QuickTree.pm
  78. 0 { → lib}/Bio/Tools/Run/Phylo/SLR.pm
  79. 0 { → lib}/Bio/Tools/Run/Phylo/Semphy.pm
  80. 0 { → lib}/Bio/Tools/Run/Primate.pm
  81. 0 { → lib}/Bio/Tools/Run/Primer3.pm
  82. 0 { → lib}/Bio/Tools/Run/Prints.pm
  83. 0 { → lib}/Bio/Tools/Run/Profile.pm
  84. 0 { → lib}/Bio/Tools/Run/Promoterwise.pm
  85. 0 { → lib}/Bio/Tools/Run/Pseudowise.pm
  86. 0 { → lib}/Bio/Tools/Run/RNAMotif.pm
  87. 0 { → lib}/Bio/Tools/Run/RepeatMasker.pm
  88. 0 { → lib}/Bio/Tools/Run/Seg.pm
  89. 0 { → lib}/Bio/Tools/Run/Signalp.pm
  90. 0 { → lib}/Bio/Tools/Run/Simprot.pm
  91. 0 { → lib}/Bio/Tools/Run/TigrAssembler.pm
  92. 0 { → lib}/Bio/Tools/Run/Tmhmm.pm
  93. 0 { → lib}/Bio/Tools/Run/TribeMCL.pm
  94. 0 { → lib}/Bio/Tools/Run/Vista.pm
  95. 0 { → lib}/Bio/Tools/Run/tRNAscanSE.pm
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0 Bio/Factory/EMBOSS.pm → lib/Bio/Factory/EMBOSS.pm
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0 Bio/Installer/Clustalw.pm → lib/Bio/Installer/Clustalw.pm
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0 Bio/Installer/EMBOSS.pm → lib/Bio/Installer/EMBOSS.pm
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0 Bio/Installer/Generic.pm → lib/Bio/Installer/Generic.pm
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0 Bio/Installer/Hyphy.pm → lib/Bio/Installer/Hyphy.pm
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0 Bio/Installer/Muscle.pm → lib/Bio/Installer/Muscle.pm
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0 Bio/Installer/PAML.pm → lib/Bio/Installer/PAML.pm
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0 Bio/Installer/Probcons.pm → lib/Bio/Installer/Probcons.pm
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0 Bio/Installer/SLR.pm → lib/Bio/Installer/SLR.pm
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0 Bio/Installer/TCoffee.pm → lib/Bio/Installer/TCoffee.pm
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0 Bio/Tools/Run/Alignment/Amap.pm → lib/Bio/Tools/Run/Alignment/Amap.pm
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0 Bio/Tools/Run/Alignment/Blat.pm → lib/Bio/Tools/Run/Alignment/Blat.pm
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0 Bio/Tools/Run/Alignment/Clustalw.pm → lib/Bio/Tools/Run/Alignment/Clustalw.pm
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0 Bio/Tools/Run/Alignment/DBA.pm → lib/Bio/Tools/Run/Alignment/DBA.pm
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0 Bio/Tools/Run/Alignment/Exonerate.pm → lib/Bio/Tools/Run/Alignment/Exonerate.pm
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0 Bio/Tools/Run/Alignment/Kalign.pm → lib/Bio/Tools/Run/Alignment/Kalign.pm
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0 Bio/Tools/Run/Alignment/Lagan.pm → lib/Bio/Tools/Run/Alignment/Lagan.pm
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0 Bio/Tools/Run/Alignment/MAFFT.pm → lib/Bio/Tools/Run/Alignment/MAFFT.pm
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0 Bio/Tools/Run/Alignment/Muscle.pm → lib/Bio/Tools/Run/Alignment/Muscle.pm
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0 Bio/Tools/Run/Alignment/Pal2Nal.pm → lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
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0 Bio/Tools/Run/Alignment/Probalign.pm → lib/Bio/Tools/Run/Alignment/Probalign.pm
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0 Bio/Tools/Run/Alignment/Probcons.pm → lib/Bio/Tools/Run/Alignment/Probcons.pm
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0 Bio/Tools/Run/Alignment/Proda.pm → lib/Bio/Tools/Run/Alignment/Proda.pm
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0 Bio/Tools/Run/Alignment/Sim4.pm → lib/Bio/Tools/Run/Alignment/Sim4.pm
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0 Bio/Tools/Run/Alignment/StandAloneFasta.pm → ...io/Tools/Run/Alignment/StandAloneFasta.pm
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0 Bio/Tools/Run/Alignment/TCoffee.pm → lib/Bio/Tools/Run/Alignment/TCoffee.pm
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0 Bio/Tools/Run/Analysis.pm → lib/Bio/Tools/Run/Analysis.pm
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0 Bio/Tools/Run/Analysis/soap.pm → lib/Bio/Tools/Run/Analysis/soap.pm
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0 Bio/Tools/Run/AnalysisFactory.pm → lib/Bio/Tools/Run/AnalysisFactory.pm
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0 Bio/Tools/Run/AnalysisFactory/soap.pm → lib/Bio/Tools/Run/AnalysisFactory/soap.pm
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0 Bio/Tools/Run/Cap3.pm → lib/Bio/Tools/Run/Cap3.pm
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0 Bio/Tools/Run/Coil.pm → lib/Bio/Tools/Run/Coil.pm
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0 Bio/Tools/Run/EMBOSSApplication.pm → lib/Bio/Tools/Run/EMBOSSApplication.pm
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0 Bio/Tools/Run/EMBOSSacd.pm → lib/Bio/Tools/Run/EMBOSSacd.pm
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0 Bio/Tools/Run/ERPIN.pm → lib/Bio/Tools/Run/ERPIN.pm
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0 Bio/Tools/Run/Ensembl.pm → lib/Bio/Tools/Run/Ensembl.pm
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0 Bio/Tools/Run/Eponine.pm → lib/Bio/Tools/Run/Eponine.pm
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0 Bio/Tools/Run/FootPrinter.pm → lib/Bio/Tools/Run/FootPrinter.pm
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0 Bio/Tools/Run/Genemark.pm → lib/Bio/Tools/Run/Genemark.pm
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0 Bio/Tools/Run/Genewise.pm → lib/Bio/Tools/Run/Genewise.pm
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0 Bio/Tools/Run/Genscan.pm → lib/Bio/Tools/Run/Genscan.pm
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0 Bio/Tools/Run/Glimmer.pm → lib/Bio/Tools/Run/Glimmer.pm
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0 Bio/Tools/Run/Hmmer.pm → lib/Bio/Tools/Run/Hmmer.pm
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0 Bio/Tools/Run/Infernal.pm → lib/Bio/Tools/Run/Infernal.pm
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0 Bio/Tools/Run/MCS.pm → lib/Bio/Tools/Run/MCS.pm
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0 Bio/Tools/Run/Match.pm → lib/Bio/Tools/Run/Match.pm
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0 Bio/Tools/Run/Mdust.pm → lib/Bio/Tools/Run/Mdust.pm
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0 Bio/Tools/Run/Meme.pm → lib/Bio/Tools/Run/Meme.pm
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0 Bio/Tools/Run/Phrap.pm → lib/Bio/Tools/Run/Phrap.pm
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0 Bio/Tools/Run/Phylo/Gerp.pm → lib/Bio/Tools/Run/Phylo/Gerp.pm
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0 Bio/Tools/Run/Phylo/Gumby.pm → lib/Bio/Tools/Run/Phylo/Gumby.pm
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0 Bio/Tools/Run/Phylo/Hyphy/Base.pm → lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
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0 Bio/Tools/Run/Phylo/Hyphy/FEL.pm → lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
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0 Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm → lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
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0 Bio/Tools/Run/Phylo/Hyphy/REL.pm → lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
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0 Bio/Tools/Run/Phylo/Hyphy/SLAC.pm → lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
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0 Bio/Tools/Run/Phylo/LVB.pm → lib/Bio/Tools/Run/Phylo/LVB.pm
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0 Bio/Tools/Run/Phylo/Molphy/ProtML.pm → lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
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0 Bio/Tools/Run/Phylo/Njtree/Best.pm → lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
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0 Bio/Tools/Run/Phylo/PAML/Baseml.pm → lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
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0 Bio/Tools/Run/Phylo/PAML/Codeml.pm → lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
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0 Bio/Tools/Run/Phylo/PAML/Evolver.pm → lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
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0 Bio/Tools/Run/Phylo/PAML/Yn00.pm → lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
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0 Bio/Tools/Run/Phylo/Phast/PhastCons.pm → lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
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0 Bio/Tools/Run/Phylo/Phast/PhyloFit.pm → lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
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0 Bio/Tools/Run/Phylo/Phylip/Base.pm → lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
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0 Bio/Tools/Run/Phylo/Phylip/Consense.pm → lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
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0 Bio/Tools/Run/Phylo/Phylip/DrawGram.pm → lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
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0 Bio/Tools/Run/Phylo/Phylip/DrawTree.pm → lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
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0 Bio/Tools/Run/Phylo/Phylip/Neighbor.pm → lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
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0 Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm → lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
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0 Bio/Tools/Run/Phylo/Phylip/ProtDist.pm → lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
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0 Bio/Tools/Run/Phylo/Phylip/ProtPars.pm → lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
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0 Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm → lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
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0 Bio/Tools/Run/Phylo/PhyloBase.pm → lib/Bio/Tools/Run/Phylo/PhyloBase.pm
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0 Bio/Tools/Run/Phylo/Phyml.pm → lib/Bio/Tools/Run/Phylo/Phyml.pm
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0 Bio/Tools/Run/Phylo/QuickTree.pm → lib/Bio/Tools/Run/Phylo/QuickTree.pm
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0 Bio/Tools/Run/Phylo/SLR.pm → lib/Bio/Tools/Run/Phylo/SLR.pm
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0 Bio/Tools/Run/Phylo/Semphy.pm → lib/Bio/Tools/Run/Phylo/Semphy.pm
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0 Bio/Tools/Run/Primate.pm → lib/Bio/Tools/Run/Primate.pm
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0 Bio/Tools/Run/Primer3.pm → lib/Bio/Tools/Run/Primer3.pm
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0 Bio/Tools/Run/Prints.pm → lib/Bio/Tools/Run/Prints.pm
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0 Bio/Tools/Run/Profile.pm → lib/Bio/Tools/Run/Profile.pm
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0 Bio/Tools/Run/Promoterwise.pm → lib/Bio/Tools/Run/Promoterwise.pm
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0 Bio/Tools/Run/Pseudowise.pm → lib/Bio/Tools/Run/Pseudowise.pm
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0 Bio/Tools/Run/RNAMotif.pm → lib/Bio/Tools/Run/RNAMotif.pm
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0 Bio/Tools/Run/RepeatMasker.pm → lib/Bio/Tools/Run/RepeatMasker.pm
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0 Bio/Tools/Run/Seg.pm → lib/Bio/Tools/Run/Seg.pm
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0 Bio/Tools/Run/Signalp.pm → lib/Bio/Tools/Run/Signalp.pm
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0 Bio/Tools/Run/Simprot.pm → lib/Bio/Tools/Run/Simprot.pm
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0 Bio/Tools/Run/TigrAssembler.pm → lib/Bio/Tools/Run/TigrAssembler.pm
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0 Bio/Tools/Run/Tmhmm.pm → lib/Bio/Tools/Run/Tmhmm.pm
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0 Bio/Tools/Run/TribeMCL.pm → lib/Bio/Tools/Run/TribeMCL.pm
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0 Bio/Tools/Run/Vista.pm → lib/Bio/Tools/Run/Vista.pm
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0 Bio/Tools/Run/tRNAscanSE.pm → lib/Bio/Tools/Run/tRNAscanSE.pm
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