[med-svn] [iqtree] branch master updated (e8d6855 -> 43436d5)

[Andreas Tille]

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tille pushed a change to branch master
in repository iqtree.

      from  e8d6855   Upload to unstable
       new  73a82c8   New upstream version 1.5.5+dfsg
       new  e020f33   Merge tag 'upstream/1.5.5+dfsg'
       new  43436d5   New upstream version

The 3 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:
 CMakeLists.txt         | 105 +++++++++----
 alignment.cpp          | 284 ++++++++++++++++++---------------
 alignment.h            |  11 +-
 checkpoint.cpp         |   4 +-
 checkpoint.h           |   9 +-
 constrainttree.cpp     |  48 ++++--
 constrainttree.h       |  15 +-
 debian/changelog       |   6 +
 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 +++-
 34 files changed, 1330 insertions(+), 725 deletions(-)

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