[med-svn] [phyml] 04/05: Updated version 3.3.20170530+dfsg from 'upstream/3.3.20170530+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository phyml.

commit 8d1f2b902a217f1da00e744449a0ed236fc3df15
Merge: 593167e 1915459
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jun 24 11:17:06 2017 +0200

    Updated version 3.3.20170530+dfsg from 'upstream/3.3.20170530+dfsg'
    
    with Debian dir 0c787c1a97528d88dc885de3dacc79818df631d6

 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(-)

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