[med-svn] [bppsuite] 06/10: Import Debian changes 0.8.0-1

[Andreas Tille]

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tille pushed a commit to branch master
in repository bppsuite.

commit 24121e8200bbf734686d274a3172edf49d749222
Merge: 5fe1288 d425f37
Author: Julien Dutheil <julien.dutheil at univ-montp2.fr>
Date:   Fri Mar 8 11:41:00 2013 +0100

    Import Debian changes 0.8.0-1
    
    bppsuite (0.8.0-1) unstable; urgency=low
    
      * New models for proteins (COaLA)
      * New program bppMixedLikelihoods

 CMakeLists.txt                                     | 183 ++++---
 ChangeLog                                          |  11 +
 .../MaximumLikelihood/Codons/BranchModel/ML.bpp    |   4 +-
 Examples/MaximumLikelihood/Codons/M0/ML.bpp        |   7 +-
 Examples/MaximumLikelihood/Codons/M1/ML.bpp        |  10 +-
 Examples/MaximumLikelihood/Codons/M2/ML.bpp        |   4 +-
 .../Nucleotides/Homogeneous/ML.bpp                 |   1 +
 Examples/Parsimony/Pars.bpp                        |   2 +
 .../{ => Homogeneous}/SeqGen.bpp                   |  16 +-
 .../{ => HomogeneousCovarion}/SeqGen.bpp           |  17 +-
 .../{ => NonHomogeneous}/SeqGen.bpp                |  27 +-
 .../SequenceSimulation/SeqGenHomogeneousModel.bpp  |   9 -
 .../SeqGenNonHomogeneousModel.bpp                  |  22 -
 bppSuite.spec                                      | 100 ----
 bppSuite/CMakeLists.txt                            |   5 +
 bppSuite/bppAlnScore.cpp                           | 335 ++++++------
 bppSuite/bppAncestor.cpp                           |  34 +-
 bppSuite/bppDist.cpp                               |  17 +-
 bppSuite/bppML.cpp                                 |  75 ++-
 bppSuite/bppMixedLikelihoods.cpp                   | 507 +++++++++++++++++
 bppSuite/bppPars.cpp                               |  31 +-
 bppSuite/bppPhyloSampler.cpp                       |  12 +-
 bppSuite/bppReRoot.cpp                             |  12 +-
 bppSuite/bppSeqGen.cpp                             |  71 ++-
 bppSuite/bppSeqMan.cpp                             |  15 +-
 bppsuite.spec                                      | 136 +++++
 debian/bppsuite.manpages                           |   1 +
 debian/changelog                                   |   7 +
 debian/control                                     |   1 +
 debian/copyright                                   |   8 +-
 debian/rules                                       |  10 +-
 doc/bppsuite.texi                                  | 598 ++++++++++++++++-----
 man/CMakeLists.txt                                 |  23 +-
 man/bppmixedlikelihoods.1.txt                      |  42 ++
 34 files changed, 1729 insertions(+), 624 deletions(-)

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