[med-svn] [iqtree] 02/03: Merge tag 'upstream/1.5.5+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository iqtree.

commit e020f33dd054386d77cd13228aa08096bce2aa67
Merge: e8d6855 73a82c8
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 19 08:47:07 2017 +0200

    Merge tag 'upstream/1.5.5+dfsg'
    
    Upstream version 1.5.5+dfsg

 CMakeLists.txt         | 105 +++++++++----
 alignment.cpp          | 284 ++++++++++++++++++---------------
 alignment.h            |  11 +-
 checkpoint.cpp         |   4 +-
 checkpoint.h           |   9 +-
 constrainttree.cpp     |  48 ++++--
 constrainttree.h       |  15 +-
 iqtree.cpp             |  33 ++--
 mexttree.cpp           |  10 +-
 mexttree.h             |   2 +-
 model/modelcodon.cpp   |  35 +++--
 model/modelfactory.cpp |  20 ++-
 model/modelfactory.h   |   4 +-
 ngs.cpp                |   2 +-
 pda.cpp                |  82 +++++-----
 phyloanalysis.cpp      | 214 +++++++++++++++++--------
 phylokernel.h          |   8 +-
 phylokernelfma.cpp     |  16 +-
 phylokernelnew.h       | 414 +++++++++++++++++++++++++++++--------------------
 phylokernelsse.cpp     |  16 +-
 phylosupertree.cpp     |   4 +-
 phylosupertreeplen.cpp |  27 +++-
 phylosupertreeplen.h   |   2 +
 phylotesting.cpp       | 104 +++++++++----
 phylotesting.h         |   9 +-
 phylotree.cpp          | 141 +++++++++++++++--
 phylotree.h            |  35 ++---
 phylotreeavx.cpp       |  16 +-
 phylotreesse.cpp       |  30 ++--
 superalignment.cpp     | 130 ++++++++++------
 superalignment.h       |   7 +
 tools.cpp              | 185 +++++++++++++---------
 tools.h                |  27 +++-
 33 files changed, 1324 insertions(+), 725 deletions(-)

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