[med-svn] [paml] branch upstream updated (4fa6da4 -> b308d0b)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository paml.

      from  4fa6da4   New upstream version 4.9c+dfsg
       new  b308d0b   New upstream version 4.9e+dfsg

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
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Summary of changes:
 README.txt                                      |   11 +-
 doc/pamlHistory.txt                             |   29 +
 doc/{pamlHistory.txt => pamlHistory.txt~}       |   23 +
 examples/DatingSoftBound/BF.Clock23.xlsx        |  Bin 0 -> 20563 bytes
 examples/DatingSoftBound/README.BayesFactor.txt |   26 +
 examples/DatingSoftBound/{ => bf1}/mcmctree.ctl |   17 +-
 examples/DatingSoftBound/{ => bf2}/mcmctree.ctl |   13 +-
 examples/DatingSoftBound/mcmctree.ctl           |    5 +-
 examples/DatingSoftBound/mtCDNApri.trees        |    4 +
 src/BFdriver.c                                  |   74 +
 src/README.txt                                  |    3 +-
 src/baseml.c                                    |    6 +-
 src/chi2.c                                      |   14 +-
 src/codeml.c                                    |    2 +-
 src/evolver.c                                   | 2630 +++++++++++------------
 src/mcmctree.c                                  |   89 +-
 src/paml.h                                      |    9 +-
 src/pamp.c                                      | 1290 +++++------
 src/tools.c                                     |  223 +-
 src/treesub.c                                   |  715 +++---
 src/yn00.c                                      | 1814 ++++++++--------
 21 files changed, 3647 insertions(+), 3350 deletions(-)
 copy doc/{pamlHistory.txt => pamlHistory.txt~} (96%)
 create mode 100644 examples/DatingSoftBound/BF.Clock23.xlsx
 create mode 100644 examples/DatingSoftBound/README.BayesFactor.txt
 copy examples/DatingSoftBound/{ => bf1}/mcmctree.ctl (67%)
 copy examples/DatingSoftBound/{ => bf2}/mcmctree.ctl (76%)
 create mode 100644 src/BFdriver.c

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