[med-svn] [bppsuite] 07/10: Updated version 2.3.1 from 'upstream/2.3.1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bppsuite.

commit 7177225abde1f7056c11980bd95a31d9c83f4f17
Merge: 457ddcd 616ba6c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 14 14:32:26 2017 +0200

    Updated version 2.3.1 from 'upstream/2.3.1'
    
    with Debian dir 4492f32840ad425a516af4d620e37435457554fe

 AUTHORS.txt                                        |   2 +
 CMakeLists.txt                                     | 302 +++------------
 ChangeLog                                          |  31 ++
 Examples/MaximumLikelihood/Codons/M1/ML.bpp        |   4 +-
 Examples/MaximumLikelihood/Codons/M2/ML.bpp        |   4 +-
 Examples/PhylogeneticSampling/PhySamp.bpp          |  54 ---
 Examples/PopStats/PopStats.bpp                     |  11 +
 Examples/PopStats/PopStatsCodonSites.bpp           |  19 +
 Examples/README                                    |   1 -
 INSTALL.txt                                        |  13 +-
 bppSuite/CMakeLists.txt                            |  86 ++--
 bppSuite/bppAlnScore.cpp                           |  44 ++-
 bppSuite/bppAncestor.cpp                           |  43 +-
 bppSuite/bppConsense.cpp                           |   8 +-
 bppSuite/bppDist.cpp                               |  24 +-
 bppSuite/bppML.cpp                                 |  61 +--
 bppSuite/bppMixedLikelihoods.cpp                   |  75 ++--
 bppSuite/bppPars.cpp                               |  11 +-
 bppSuite/bppPhyloSampler.cpp                       | 282 --------------
 bppSuite/bppPopStats.cpp                           | 421 ++++++++++++++++++++
 bppSuite/bppReRoot.cpp                             |  10 +-
 bppSuite/bppSeqGen.cpp                             | 208 +++++++---
 bppSuite/bppSeqMan.cpp                             |  77 ++--
 bppSuite/bppTreeDraw.cpp                           |  20 +-
 bppsuite.spec                                      |  80 ++--
 buildBin.sh                                        |   5 +-
 doc/CMakeLists.txt                                 |  76 +++-
 doc/bppsuite.texi                                  | 431 ++++++++++++++++-----
 man/CMakeLists.txt                                 |  54 ++-
 man/{bppalnscore.1.txt => bppalnscore.1}           |   0
 man/{bppancestor.1.txt => bppancestor.1}           |   0
 man/{bppconsense.1.txt => bppconsense.1}           |   0
 man/{bppdist.1.txt => bppdist.1}                   |   0
 ...ixedlikelihoods.1.txt => bppmixedlikelihoods.1} |   0
 man/{bppml.1.txt => bppml.1}                       |   0
 man/{bpppars.1.txt => bpppars.1}                   |   0
 man/bppphysamp.1.txt                               |  37 --
 man/{bppreroot.1.txt => bpppopstats.1}             |  10 +-
 man/{bppreroot.1.txt => bppreroot.1}               |   0
 man/{bppseqgen.1.txt => bppseqgen.1}               |   0
 man/{bppseqman.1.txt => bppseqman.1}               |   0
 man/{bpptreedraw.1.txt => bpptreedraw.1}           |   0
 42 files changed, 1455 insertions(+), 1049 deletions(-)

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