[med-svn] [physamp] branch upstream updated (4c0161b -> d50a940)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository physamp.

      from  4c0161b   Imported Upstream version 0.2.0
       new  d50a940   New upstream version 1.0.1

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:
 AUTHORS.txt => AUTHORS                   |    0
 CMakeLists.txt                           |  258 +---
 INSTALL.txt => INSTALL                   |    0
 COPYING.txt => LICENSE                   |    9 +-
 _config.yml                              |    1 +
 buildBin.sh                              |    7 +
 doc/CMakeLists.txt                       |    7 -
 docs/CMakeLists.txt                      |   73 ++
 docs/_config.yml                         |    1 +
 docs/index.md                            |   35 +
 {doc => docs}/physamp.texi               |   58 +-
 examples/LSU/LSU.dnd                     |    1 +
 examples/LSU/LSU.phy                     | 1976 ++++++++++++++++++++++++++++++
 examples/LSU/PhySamp.bpp                 |   54 +
 examples/PF01049/runFasttree.sh          |    3 +
 man/CMakeLists.txt                       |   39 +-
 man/{bppalnoptim.1.txt => bppalnoptim.1} |    2 +-
 physamp.spec                             |   87 ++
 physamp/AlignmentOptimizer.cpp           |   12 +-
 physamp/CMakeLists.txt                   |   27 +-
 physamp/PhyloSampler.cpp                 |  267 ++++
 21 files changed, 2677 insertions(+), 240 deletions(-)
 rename AUTHORS.txt => AUTHORS (100%)
 rename INSTALL.txt => INSTALL (100%)
 rename COPYING.txt => LICENSE (99%)
 create mode 100644 _config.yml
 create mode 100755 buildBin.sh
 delete mode 100644 doc/CMakeLists.txt
 create mode 100644 docs/CMakeLists.txt
 create mode 100644 docs/_config.yml
 create mode 100644 docs/index.md
 rename {doc => docs}/physamp.texi (79%)
 create mode 100644 examples/LSU/LSU.dnd
 create mode 100644 examples/LSU/LSU.phy
 create mode 100644 examples/LSU/PhySamp.bpp
 create mode 100755 examples/PF01049/runFasttree.sh
 rename man/{bppalnoptim.1.txt => bppalnoptim.1} (97%)
 create mode 100644 physamp.spec
 create mode 100755 physamp/PhyloSampler.cpp

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