[med-svn] [iqtree] 02/03: Merge tag 'upstream/1.4.2+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository iqtree.

commit 8f721949e0ace5dd76043009c4eda775e82b4f0b
Merge: 5abbd97 a68a042
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 24 21:49:41 2016 +0200

    Merge tag 'upstream/1.4.2+dfsg'
    
    Upstream version 1.4.2+dfsg

 CMakeLists.txt            |   2 +-
 alignment.cpp             |   4 +-
 alignment.h               |   4 +-
 iqtree.cpp                | 114 +++++----
 model/modelfactory.cpp    | 124 +++++++++-
 model/modelfactory.h      |   8 +
 model/modelgtr.cpp        |   1 +
 model/partitionmodel.cpp  |  33 +++
 model/partitionmodel.h    |   8 +
 model/ratefree.cpp        |   1 +
 model/ratefree.h          |   2 +-
 model/ratefreeinvar.cpp   |   2 +-
 model/rategamma.cpp       |   1 +
 model/rategamma.h         |   2 +-
 model/rategammainvar.cpp  |  36 ++-
 model/rategammainvar.h    |   9 +
 model/rateheterogeneity.h |  16 ++
 model/rateinvar.cpp       |   6 +-
 model/ratekategory.cpp    |   1 +
 msetsblock.cpp            |   1 +
 pda.cpp                   |   2 +-
 phyloanalysis.cpp         |  34 +--
 phylosupertreeplen.cpp    |   7 +
 phylosupertreeplen.h      |   9 +
 phylotesting.cpp          |  41 +++-
 phylotree.cpp             |   5 +-
 phylotree.h               |  34 +--
 quartet.cpp               | 611 +++++++++++++++++++++++++---------------------
 superalignment.cpp        |  20 +-
 superalignment.h          |   4 +-
 tools.cpp                 |  52 +++-
 tools.h                   |  23 +-
 32 files changed, 811 insertions(+), 406 deletions(-)

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