[med-svn] [bppsuite] branch upstream updated (1268477 -> 616ba6c)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository bppsuite.

      from  1268477   Import Upstream version 2.2.0
       new  616ba6c   New upstream version 2.3.1

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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 +-
 debian/bppsuite.manpages                           |  11 -
 debian/changelog                                   |  73 ----
 debian/compat                                      |   1 -
 debian/control                                     |  27 --
 debian/copyright                                   |  62 ---
 debian/docs                                        |   0
 debian/rules                                       | 155 --------
 debian/source/format                               |   1 -
 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/{bpppars.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
 50 files changed, 1455 insertions(+), 1379 deletions(-)
 delete mode 100755 Examples/PhylogeneticSampling/PhySamp.bpp
 create mode 100644 Examples/PopStats/PopStats.bpp
 create mode 100644 Examples/PopStats/PopStatsCodonSites.bpp
 delete mode 100755 bppSuite/bppPhyloSampler.cpp
 create mode 100644 bppSuite/bppPopStats.cpp
 delete mode 100644 debian/bppsuite.manpages
 delete mode 100644 debian/changelog
 delete mode 100644 debian/compat
 delete mode 100644 debian/control
 delete mode 100644 debian/copyright
 delete mode 100644 debian/docs
 delete mode 100755 debian/rules
 delete mode 100644 debian/source/format
 rename man/{bppalnscore.1.txt => bppalnscore.1} (100%)
 rename man/{bppancestor.1.txt => bppancestor.1} (100%)
 rename man/{bppconsense.1.txt => bppconsense.1} (100%)
 rename man/{bppdist.1.txt => bppdist.1} (100%)
 rename man/{bppmixedlikelihoods.1.txt => bppmixedlikelihoods.1} (100%)
 rename man/{bppml.1.txt => bppml.1} (100%)
 copy man/{bpppars.1.txt => bpppars.1} (100%)
 delete mode 100644 man/bppphysamp.1.txt
 rename man/{bpppars.1.txt => bpppopstats.1} (59%)
 rename man/{bppreroot.1.txt => bppreroot.1} (100%)
 rename man/{bppseqgen.1.txt => bppseqgen.1} (100%)
 rename man/{bppseqman.1.txt => bppseqman.1} (100%)
 rename man/{bpptreedraw.1.txt => bpptreedraw.1} (100%)

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