[med-svn] [iqtree] branch upstream updated (79edd15 -> 35c46f5)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository iqtree.

      from  79edd15   Imported Upstream version 1.3.14+dfsg
       new  35c46f5   Imported Upstream version 1.4.0+dfsg

The 1 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 ++++++++-
 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 +-
 75 files changed, 7814 insertions(+), 1014 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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