[med-svn] [iqtree] branch master updated (e8b9f92 -> b59ce0c)

[Andreas Tille]

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tille pushed a change to branch master
in repository iqtree.

      from  e8b9f92   Merge tag 'upstream/1.3.14+dfsg'
       new  4c99d87   Imported Upstream version 1.4.0+dfsg
       new  1bc8ee3   Refresh patches
       new  b59ce0c   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                  |   17 +-
 alignment.cpp                   |   90 +-
 alignment.h                     |    5 +-
 candidateset.cpp                |   61 +-
 candidateset.h                  |   13 +-
 checkpoint.cpp                  |  274 +++---
 checkpoint.h                    |  348 +++++++-
 debian/changelog                |    4 +-
 debian/patches/32bit_name.patch |    2 +-
 debian/patches/avoid_mavx.patch |    2 +-
 debian/patches/sse.patch        |    4 +-
 gsl/CMakeLists.txt              |    8 +
 gsl/binomial_tpe.cpp            |  381 +++++++++
 gsl/gauss.cpp                   |  352 ++++++++
 gsl/gaussinv.cpp                |  205 +++++
 gsl/gausspdf.cpp                |   40 +
 gsl/gsl_nan.h                   |   45 +
 gsl/multinomial.cpp             |   82 ++
 gsl/mygsl.h                     |   57 ++
 gsl/pow_int.cpp                 |   56 ++
 gsl/rat_eval.h                  |   25 +
 hashsplitset.cpp                |    8 +-
 iqtree.cpp                      |  736 +++++++---------
 iqtree.h                        |   34 +-
 model/modelcodon.cpp            |   41 +
 model/modelcodon.h              |   10 +
 model/modeldna.cpp              |   17 +
 model/modeldna.h                |   10 +
 model/modelfactory.cpp          |  103 ++-
 model/modelfactory.h            |   22 +-
 model/modelgtr.cpp              |   17 +-
 model/modelgtr.h                |   10 +
 model/modelmixture.cpp          |   63 +-
 model/modelmixture.h            |   16 +
 model/modelsubst.cpp            |   34 +-
 model/modelsubst.h              |   17 +-
 model/partitionmodel.cpp        |   38 +
 model/partitionmodel.h          |   18 +
 model/ratefree.cpp              |   24 +
 model/ratefree.h                |   10 +
 model/ratefreeinvar.cpp         |   14 +
 model/ratefreeinvar.h           |   10 +
 model/rategamma.cpp             |   22 +
 model/rategamma.h               |   10 +
 model/rategammainvar.cpp        |   17 +
 model/rategammainvar.h          |   10 +
 model/rateheterogeneity.cpp     |   17 +-
 model/rateheterogeneity.h       |   13 +-
 model/rateinvar.cpp             |   18 +
 model/rateinvar.h               |   10 +
 mtree.cpp                       |   10 +-
 mtree.h                         |    2 +-
 optimization.cpp                |    2 +-
 optimization.h                  |    3 +-
 pda.cpp                         |  105 ++-
 phyloanalysis.cpp               |  298 ++++---
 phyloanalysis.h                 |    2 +-
 phylokernel.h                   |    7 +
 phylokernelsitemodel.cpp        |  715 ++++++++++++++++
 phylokernelsitemodel.h          |  801 ++++++++++++++++++
 phylosupertree.cpp              |   53 +-
 phylosupertree.h                |   16 +
 phylosupertreeplen.cpp          |   43 +
 phylosupertreeplen.h            |   20 +
 phylotesting.cpp                |  369 +++++++-
 phylotesting.h                  |    8 +
 phylotree.cpp                   |  181 +++-
 phylotree.h                     |  152 +++-
 phylotreeavx.cpp                |   26 +
 phylotreesse.cpp                |  464 ++++++++---
 quartet.cpp                     | 1756 +++++++++++++++++++++++++++++++++++++++
 splitgraph.cpp                  |   65 ++
 splitgraph.h                    |   19 +-
 stoprule.cpp                    |   22 +-
 stoprule.h                      |   14 +-
 superalignment.cpp              |   61 +-
 superalignment.h                |   11 +-
 tools.cpp                       |  135 ++-
 tools.h                         |   40 +-
 79 files changed, 7820 insertions(+), 1020 deletions(-)
 create mode 100644 gsl/CMakeLists.txt
 create mode 100644 gsl/binomial_tpe.cpp
 create mode 100644 gsl/gauss.cpp
 create mode 100644 gsl/gaussinv.cpp
 create mode 100644 gsl/gausspdf.cpp
 create mode 100644 gsl/gsl_nan.h
 create mode 100644 gsl/multinomial.cpp
 create mode 100644 gsl/mygsl.h
 create mode 100644 gsl/pow_int.cpp
 create mode 100644 gsl/rat_eval.h
 create mode 100644 phylokernelsitemodel.cpp
 create mode 100644 phylokernelsitemodel.h
 create mode 100644 quartet.cpp

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