[med-svn] [seq-gen] branch upstream updated (8cfb759 -> 95dced2)

[Alex Mestiashvili]

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malex-guest pushed a change to branch upstream
in repository seq-gen.

      from  8cfb759   New upstream version 1.3.3+git4a8cc9d.ds
       new  95dced2   New upstream version 1.3.4

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:
 .gitignore                        |   5 +
 documentation/Seq-Gen.Manual.html |  55 +++++++++-
 examples/seqs+trees.phy           |   7 ++
 source/aamodels.c                 |   4 +-
 source/aamodels.h                 |   4 +-
 source/eigen.c                    |   4 +-
 source/eigen.h                    |   4 +-
 source/evolve.c                   |   4 +-
 source/evolve.h                   |   4 +-
 source/gamma.c                    |   4 +-
 source/gamma.h                    |   4 +-
 source/global.c                   |   9 +-
 source/global.h                   |   4 +-
 source/model.c                    |   4 +-
 source/model.h                    |   4 +-
 source/nucmodels.c                |   4 +-
 source/nucmodels.h                |   4 +-
 source/progress.c                 |   4 +-
 source/progress.h                 |   4 +-
 source/seq-gen.c                  | 213 +++++++++++++++++++++-----------------
 source/tree.h                     |   4 +-
 source/treefile.c                 |  14 +--
 source/treefile.h                 |   4 +-
 source/twister.c                  |   4 +-
 source/twister.h                  |   4 +-
 25 files changed, 231 insertions(+), 148 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 examples/seqs+trees.phy

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