[med-svn] [phyml] branch master updated (6084400 -> 58e2901)

[Kevin Murray]

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

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

      from  6084400   Fix watch link to github archives
      adds  ba9f9cc   Imported Upstream version 20141029+dfsg
       new  9f4c57b   Imported Upstream version 3.2.0+dfsg
       new  dd9c17c   Merge tag 'upstream/3.2.0+dfsg'
       new  fdf4088   New version in d/ch
       new  32c7b94   Add myself to uploaders
       new  d9e979a   Fix typo in README.debian
       new  1b2ee39   target unstable
       new  8a5717a   Build missing symbols by adding -DPHYREX to CFLAGS
       new  58e2901   Nuke out of date upstream metadata

The 8 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:
 .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 +
 debian/README.Debian         |    2 +-
 debian/changelog             |    7 +
 debian/control               |    3 +-
 debian/rules                 |    2 +-
 debian/upstream/metadata     |    8 -
 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 +
 68 files changed, 18532 insertions(+), 11164 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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