[med-svn] [iqtree] 02/04: Merge tag 'upstream/1.4.3+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository iqtree.

commit 45ea2202cc4032066e2aaa4bcb9f82ca8e4652aa
Merge: 4709d4d d67f0c4
Author: Andreas Tille <tille at debian.org>
Date:   Mon Aug 15 22:23:01 2016 +0200

    Merge tag 'upstream/1.4.3+dfsg'
    
    Upstream version 1.4.3+dfsg

 CMakeLists.txt              |    2 +-
 alignment.cpp               |   88 +++-
 alignment.h                 |   14 +-
 checkpoint.cpp              |    4 +-
 iqtree.cpp                  |   45 +-
 model/modelcodon.cpp        |   75 +++
 model/modelcodon.h          |   10 +
 model/modeldna.cpp          |   10 +-
 model/modelfactory.cpp      |  414 +++++++--------
 model/modelfactory.h        |    8 +-
 model/modelgtr.cpp          |    8 +-
 model/modelgtr.h            |    2 +-
 model/modelmixture.cpp      |    2 +-
 model/modelnonrev.cpp       |    6 +-
 model/ratefree.cpp          |   28 +-
 model/ratefreeinvar.cpp     |    1 +
 model/ratefreeinvar.h       |    2 +-
 model/rategamma.cpp         |   29 +-
 model/rategammainvar.cpp    |  239 ++++++---
 model/rategammainvar.h      |   53 +-
 model/rateheterogeneity.cpp |   18 +-
 model/rateheterogeneity.h   |   13 +
 ncl/nxscharactersblock.cpp  |    9 +-
 ngs.cpp                     |    4 +-
 ngs.h                       |    2 +-
 pda.cpp                     |    2 -
 phyloanalysis.cpp           |   53 +-
 phylokernel.h               |   10 +-
 phylokernelmixrate.h        |    6 +
 phylokernelmixture.h        |    6 +
 phylosupertreeplen.cpp      |    6 +-
 phylotesting.cpp            |   69 ++-
 phylotree.cpp               | 1162 ++----------------------------------------
 phylotree.h                 |  152 +-----
 phylotreesse.cpp            | 1185 ++++++++++++++++---------------------------
 quartet.cpp                 |    4 +
 tools.cpp                   |  122 +++--
 tools.h                     |   33 +-
 38 files changed, 1425 insertions(+), 2471 deletions(-)

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