[med-svn] [paml] branch master updated (99e336b -> 05cecb3)

[Andreas Tille]

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tille pushed a change to branch master
in repository paml.

      from  99e336b   Upstream has released a new version mentioning GPL in some file but not all.  Need to clarify again
       new  b308d0b   New upstream version 4.9e+dfsg
       new  2371206   Merge tag 'upstream/4.9e+dfsg'
       new  05cecb3   This new upstream version is now covered by a free license and can be released to main

The 3 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:
 README.txt                                      |   11 +-
 debian/changelog                                |    7 +
 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 ++++++++--------
 22 files changed, 3654 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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