[med-svn] [iqtree] 02/04: Merge tag 'upstream/1.4.4+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository iqtree.

commit ea8cbe36c687d90264e3c48a7d85de0680b79c9f
Merge: 2190669 cda5433
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 9 11:05:34 2016 +0200

    Merge tag 'upstream/1.4.4+dfsg'
    
    Upstream version 1.4.4+dfsg

 CMakeLists.txt              |  11 +-
 alignment.cpp               | 209 ++++++++++++++----
 alignment.h                 |  23 ++
 checkpoint.cpp              |  42 +++-
 checkpoint.h                |  18 ++
 gzstream.cpp                |   5 +-
 gzstream.h                  |   2 +
 iqtree.cpp                  |  10 +-
 iqtree.h                    |   4 +-
 model/modelcodon.cpp        |  30 +++
 model/modelfactory.cpp      | 191 ++++++-----------
 model/modelfactory.h        |  27 ++-
 model/modelgtr.cpp          |  84 ++++----
 model/modelgtr.h            |  14 +-
 model/modelmixture.cpp      |  86 ++++++--
 model/modelmixture.h        |  11 +
 model/modelprotein.cpp      |  38 +++-
 model/modelprotein.h        |  10 +
 model/modelset.cpp          |   4 +-
 model/modelset.h            |  13 +-
 model/modelsubst.h          |   8 +
 model/partitionmodel.cpp    |   4 +-
 model/partitionmodel.h      |  11 +-
 model/ratemeyerhaeseler.cpp |   6 +-
 modelsblock.h               |  11 +-
 mpdablock.cpp               |   2 +-
 msplitsblock.cpp            |   2 +-
 mtreeset.cpp                |   4 +-
 ncl/nxscharactersblock.cpp  |   1 +
 ncl/nxsdistancesblock.cpp   |   1 +
 ncl/nxstaxablock.cpp        |   1 +
 pattern.cpp                 |  10 +-
 pattern.h                   |  22 +-
 pda.cpp                     |  94 ++++++---
 phyloanalysis.cpp           | 336 ++++++++++++++++++++---------
 phylokernel.h               |   4 +
 phylokernelsitemodel.cpp    | 230 ++++++++++----------
 phylokernelsitemodel.h      |   6 +
 phylosupertree.cpp          |  24 ++-
 phylosupertree.h            |  12 ++
 phylosupertreeplen.cpp      |  24 ++-
 phylosupertreeplen.h        |  12 +-
 phylotesting.cpp            | 505 ++++++++++++++++++++++++++++++++++++++------
 phylotesting.h              |   9 +-
 phylotree.cpp               | 122 ++++++++---
 phylotree.h                 |  20 +-
 pll/pll.h                   |   2 +-
 pruning.h                   |   2 +-
 tinatree.cpp                |   2 +-
 tools.cpp                   | 131 +++++++++---
 tools.h                     |  63 +++++-
 51 files changed, 1837 insertions(+), 676 deletions(-)

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