[med-svn] [phyml] branch upstream updated (cf20f11 -> a845584)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository phyml.

      from  cf20f11   Imported Upstream version 3.2.20160530+dfsg
       new  a845584   Imported Upstream version 3.2.0+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:
 NEWS                                      |    0
 README                                    |   30 +-
 autogen.sh                                |    0
 config.h.in                               |    3 -
 configure.ac                              |   24 +-
 doc/fig/phyrexlog.pdf                     |  Bin 463638 -> 0 bytes
 doc/phyml-manual.pdf                      |  Bin 885797 -> 407931 bytes
 doc/phyml-manual.tex                      |  135 +-
 doc/ref.bib                               |   74 -
 examples/phyrex_input_files/h1n1.nxs      |  613 -------
 examples/phyrex_input_files/usa_coord.txt |   53 -
 src/Makefile.am                           |   90 +-
 src/alrt.c                                |  262 +--
 src/cl.c                                  |  109 +-
 src/cl.h                                  |    1 -
 src/date.c                                |  789 --------
 src/date.h                                |   41 -
 src/free.c                                |  230 +--
 src/free.h                                |   12 +-
 src/init.c                                |  300 ++-
 src/init.h                                |   10 +-
 src/interface.c                           |   27 +-
 src/invitee.c                             |   60 +-
 src/invitee.h                             |    2 +-
 src/io.c                                  | 1666 +++++++++++++----
 src/io.h                                  |    7 -
 src/lk.c                                  |  958 +++++-----
 src/m4.c                                  |    6 +-
 src/main.c                                |   29 +-
 src/make.c                                |  143 +-
 src/make.h                                |   12 +-
 src/mcmc.c                                |  370 +---
 src/mcmc.h                                |    5 +-
 src/mg.c                                  | 2820 +++++++++++++++++++++++++++++
 src/mg.h                                  |   51 +
 src/mixt.c                                |  829 ++-------
 src/mixt.h                                |   16 +-
 src/models.c                              |   16 +-
 src/mpi_boot.c                            |    2 +-
 src/optimiz.c                             |  221 +--
 src/pars.c                                |  182 +-
 src/phyrex.c                              |  375 ++--
 src/phyrex.h                              |    4 +-
 src/rates.c                               |    8 +-
 src/simu.c                                |  715 ++++----
 src/spr.c                                 | 1237 ++++++-------
 src/spr.h                                 |   14 +-
 src/stats.c                               |   13 +-
 src/stats.h                               |    2 +-
 src/times.c                               |  507 +-----
 src/times.h                               |    3 -
 src/utilities.c                           | 2358 ++++++++++--------------
 src/utilities.h                           |  193 +-
 src/xml.c                                 | 1146 +-----------
 src/xml.h                                 |    3 -
 55 files changed, 7548 insertions(+), 9228 deletions(-)
 create mode 100644 NEWS
 mode change 100755 => 100644 autogen.sh
 delete mode 100644 doc/fig/phyrexlog.pdf
 delete mode 100644 examples/phyrex_input_files/h1n1.nxs
 delete mode 100644 examples/phyrex_input_files/usa_coord.txt
 delete mode 100644 src/date.c
 delete mode 100644 src/date.h

-- 
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