[med-svn] [bppsuite] 04/10: Import Debian changes 0.7.0-1

[Andreas Tille]

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tille pushed a commit to branch master
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commit 5fe12885bb6ebae1aa5e5824b4888d276ff2ba12
Merge: 2382145 5b3e480
Author: Julien Dutheil <julien.dutheil at univ-montp2.fr>
Date:   Wed Feb 15 09:17:00 2012 +0100

    Import Debian changes 0.7.0-1
    
    bppsuite (0.7.0-1) unstable; urgency=low
    
      * Several program improvements (more models, options, etc.)
      * New program bpp Alignment scores.

 CMakeLists.txt                                     |   11 +-
 ChangeLog                                          |    9 +
 Examples/AlignmentScoring/AlnScores.bpp            |   13 +
 Examples/Data/HIV1_REF_2010_gag_DNA.fasta          | 1638 ++++++++++++++++++++
 Examples/Data/HIV1_REF_2010_gag_macse_AA.fasta     |   78 +
 Examples/Data/HIV1_REF_2010_gag_macse_DNA.fasta    |   78 +
 .../MaximumLikelihood/Codons/BranchModel/ML.bpp    |    2 +-
 .../Codons/{BranchModel => M0}/ML.bpp              |   14 +-
 .../Codons/{BranchModel => M1}/ML.bpp              |   20 +-
 .../Codons/{BranchModel => M2}/ML.bpp              |   20 +-
 .../Nucleotides/Homogeneous/ML.bpp                 |    6 +-
 .../Nucleotides/NonHomogeneousGG/MLNHGG.bpp        |    8 +-
 .../Nucleotides/NonHomogeneousGeneral/MLNH.bpp     |   31 +-
 .../MaximumLikelihood/Proteins/Homogeneous/ML.bpp  |    6 +-
 Examples/README                                    |    5 +
 Examples/SequenceManipulation/SeqMan2.bpp          |   33 +
 Examples/SequenceSimulation/SeqGen.bpp             |    2 +-
 bppSuite.spec                                      |    7 +-
 bppSuite/CMakeLists.txt                            |    5 +
 bppSuite/bppAlnScore.cpp                           |  226 +++
 bppSuite/bppAncestor.cpp                           |  268 ++--
 bppSuite/bppML.cpp                                 |  280 ++--
 bppSuite/bppSeqMan.cpp                             |  100 +-
 debian/changelog                                   |    7 +
 debian/control                                     |    6 +-
 doc/bppsuite.texi                                  |  700 ++++++---
 doc/version.texi                                   |    2 -
 man/CMakeLists.txt                                 |    1 +
 man/bppalnscore.1.txt                              |   39 +
 29 files changed, 3048 insertions(+), 567 deletions(-)

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