[med-svn] [phyml] 06/07: Merge tag 'upstream/3.2.20160530+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository phyml.

commit 6d1664305f7fe7a72c4cf614df68fa55244f5135
Merge: 4088c36 cf20f11
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jul 20 09:36:38 2016 +0200

    Merge tag 'upstream/3.2.20160530+dfsg'
    
    Upstream version 3.2.20160530+dfsg

 NEWS                                      |    0
 README                                    |   30 +-
 autogen.sh                                |    0
 config.h.in                               |    3 +
 configure.ac                              |   24 +-
 doc/fig/phyrexlog.pdf                     |  Bin 0 -> 463638 bytes
 doc/phyml-manual.pdf                      |  Bin 407931 -> 885797 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, 9228 insertions(+), 7548 deletions(-)

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