[med-svn] [iqtree] branch master updated (2190669 -> b5cfc5f)

[Andreas Tille]

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tille pushed a change to branch master
in repository iqtree.

      from  2190669   Upload to unstable
       new  cda5433   New upstream version 1.4.4+dfsg
       new  ea8cbe3   Merge tag 'upstream/1.4.4+dfsg'
       new  226aa9a   New upstream version
       new  b5cfc5f   Update + deactivate patches

The 4 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                  |  11 +-
 alignment.cpp                   | 209 ++++++++++++++---
 alignment.h                     |  23 ++
 checkpoint.cpp                  |  42 +++-
 checkpoint.h                    |  18 ++
 debian/changelog                |   7 +
 debian/patches/32bit_name.patch |   2 +-
 debian/patches/series           |   3 +-
 debian/patches/spelling.patch   |  91 --------
 debian/patches/sse.patch        |  32 +--
 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 ++++-
 56 files changed, 1851 insertions(+), 797 deletions(-)
 delete mode 100644 debian/patches/spelling.patch

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