[med-svn] [phyml] branch upstream updated (a845584 -> 1915459)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository phyml.

      from  a845584   Imported Upstream version 3.2.0+dfsg
       new  1915459   New upstream version 3.3.20170530+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:
 ChangeLog                                 |  347 --
 NEWS                                      |    0
 README                                    |   31 +-
 autogen.sh                                |    0
 config.h.in                               |   10 +-
 configure.ac                              |   74 +-
 doc/fig/phyrexlog.pdf                     |  Bin 0 -> 463638 bytes
 doc/phyml-manual.pdf                      |  Bin 407931 -> 870332 bytes
 doc/phyml-manual.tex                      |  567 ++--
 doc/ref.bib                               |  190 +-
 examples/phyrex_input_files/h1n1.nxs      |  613 ++++
 examples/phyrex_input_files/usa_coord.txt |   53 +
 src/Makefile.am                           |  171 +-
 src/alrt.c                                |  401 +--
 src/avx.c                                 |  424 +++
 src/avx.h                                 |   39 +
 src/beagle_utils.c                        |    8 +-
 src/bionj.c                               |   26 +-
 src/cl.c                                  |  171 +-
 src/cl.h                                  |    1 +
 src/date.c                                | 1249 +++++++
 src/date.h                                |   44 +
 src/draw.c                                |   14 +-
 src/eigen.c                               |   70 +-
 src/free.c                                |  382 ++-
 src/free.h                                |   14 +-
 src/geo.c                                 |  139 +-
 src/help.c                                |    2 +-
 src/init.c                                |  526 +--
 src/init.h                                |   11 +-
 src/interface.c                           |   92 +-
 src/invitee.c                             |  191 +-
 src/invitee.h                             |    2 +-
 src/io.c                                  | 2708 ++++++---------
 src/io.h                                  |   12 +-
 src/lk.c                                  | 3630 ++++++++++----------
 src/lk.h                                  |   75 +-
 src/m4.c                                  |  230 +-
 src/m4.h                                  |    4 +-
 src/main.c                                |  104 +-
 src/make.c                                |  325 +-
 src/make.h                                |   13 +-
 src/mcmc.c                                | 4294 +++++++++++++++++-------
 src/mcmc.h                                |   15 +-
 src/mg.c                                  | 2820 ----------------
 src/mg.h                                  |   51 -
 src/mixt.c                                | 1986 ++++++++---
 src/mixt.h                                |   39 +-
 src/models.c                              |  569 ++--
 src/models.h                              |    5 +-
 src/mpi_boot.c                            |  138 +-
 src/nexus.c                               |   12 +-
 src/optimiz.c                             | 1735 +++++-----
 src/optimiz.h                             |   10 +-
 src/pars.c                                |  497 ++-
 src/pars.h                                |    7 +-
 src/phyrex.c                              | 1598 ++++++---
 src/phyrex.h                              |    5 +-
 src/rates.c                               |  635 ++--
 src/rates.h                               |    2 +
 src/rwrapper.c                            |    6 +-
 src/simu.c                                | 1118 ++++---
 src/simu.h                                |    1 +
 src/spr.c                                 | 5201 ++++++++---------------------
 src/spr.h                                 |   19 +-
 src/sse.c                                 |  406 +++
 src/sse.h                                 |   36 +
 src/stats.c                               |  606 ++--
 src/stats.h                               |    2 +-
 src/times.c                               | 1001 ++++--
 src/times.h                               |    8 +-
 src/tiporder.c                            |  122 +-
 src/utilities.c                           | 4849 +++++++++++++++------------
 src/utilities.h                           |  429 ++-
 src/xml.c                                 | 1169 ++++++-
 src/xml.h                                 |    3 +
 76 files changed, 22970 insertions(+), 19387 deletions(-)
 delete mode 100644 NEWS
 mode change 100644 => 100755 autogen.sh
 create mode 100644 doc/fig/phyrexlog.pdf
 create mode 100644 examples/phyrex_input_files/h1n1.nxs
 create mode 100644 examples/phyrex_input_files/usa_coord.txt
 create mode 100644 src/avx.c
 create mode 100644 src/avx.h
 create mode 100644 src/date.c
 create mode 100644 src/date.h
 create mode 100644 src/sse.c
 create mode 100644 src/sse.h

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