[med-svn] [phyml] branch upstream updated (ba9f9cc -> 9f4c57b)

[Kevin Murray]

This is an automated email from the git hooks/post-receive script.

daube-guest pushed a change to branch upstream
in repository phyml.

      from  ba9f9cc   Imported Upstream version 20141029+dfsg
      adds  9f4c57b   Imported Upstream version 3.2.0+dfsg

No new revisions were added by this update.

Summary of changes:
 .gitignore                   |   29 +
 COPYING => LICENSE           |   47 +-
 README                       |   16 +-
 README.md                    |    6 +
 autogen.sh                   |    2 +
 config.h.in                  |   12 +-
 configure.ac                 |   29 +-
 confmc                       |    9 +
 confr                        |    9 +
 confrf                       |    9 +
 doc/example.html             | 1331 ----------
 doc/example.text             | 2812 ---------------------
 doc/naturemag.bst            | 3049 ++++++++++++-----------
 doc/phyml-manual.pdf         |  Bin 392421 -> 407931 bytes
 doc/phyml-manual.tex         |   21 +-
 doc/ref.bib                  | 5534 +++++++++++++++++++++++++++++++++++++++++-
 examples/X1.mat              |   21 -
 src/Makefile.am              |   29 +-
 src/Makefile_mc.am           |   39 +
 src/Makefile_r.am            |   86 +
 src/alrt.c                   |    2 +-
 src/bionj.c                  |   14 +-
 src/bionj.h                  |    2 +-
 src/cl.c                     |   95 +-
 src/cl.h                     |    2 +-
 src/free.c                   |   72 +-
 src/free.h                   |    2 +
 src/geo.c                    |    1 -
 src/help.c                   |    5 +-
 src/init.c                   |  362 ++-
 src/init.h                   |    8 +-
 src/interface.c              |    6 +-
 src/{sergeii.c => invitee.c} |    4 +-
 src/{sergeii.h => invitee.h} |    4 +-
 src/io.c                     |  590 +++--
 src/io.h                     |    2 +-
 src/lk.c                     |  507 ++--
 src/main.c                   |   58 +-
 src/make.c                   |  159 +-
 src/make.h                   |    9 +-
 src/mcmc.c                   | 4640 +++++++++++++++++++++++------------
 src/mcmc.h                   |   47 +-
 src/mg.c                     |    2 +-
 src/migrep.c                 | 1819 --------------
 src/migrep.h                 |   59 -
 src/mixt.c                   |   23 +-
 src/models.c                 |  106 +-
 src/mpi_boot.c               |    4 +-
 src/mxml.h                   |  329 +++
 src/nexus.c                  |   17 +-
 src/optimiz.c                | 1163 ++++-----
 src/phyrex.c                 | 4173 +++++++++++++++++++++++++++++++
 src/phyrex.h                 |  113 +
 src/rates.c                  |    4 +-
 src/simu.c                   |   42 +-
 src/spr.c                    |   12 +-
 src/stats.c                  |  980 +++++++-
 src/stats.h                  |   25 +
 src/times.c                  |   23 +-
 src/utilities.c              |  921 ++++---
 src/utilities.h              |  167 +-
 src/xml.c                    |   10 +-
 version                      |    1 +
 63 files changed, 18521 insertions(+), 11153 deletions(-)
 create mode 100644 .gitignore
 copy COPYING => LICENSE (95%)
 create mode 100644 README.md
 create mode 100644 autogen.sh
 create mode 100755 confmc
 create mode 100755 confr
 create mode 100755 confrf
 delete mode 100644 doc/example.html
 delete mode 100644 doc/example.text
 delete mode 100644 examples/X1.mat
 create mode 100644 src/Makefile_mc.am
 create mode 100644 src/Makefile_r.am
 rename src/{sergeii.c => invitee.c} (99%)
 rename src/{sergeii.h => invitee.h} (98%)
 delete mode 100644 src/migrep.c
 delete mode 100644 src/migrep.h
 create mode 100644 src/mxml.h
 create mode 100644 src/phyrex.c
 create mode 100644 src/phyrex.h
 create mode 100644 version

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