[med-svn] [physamp] branch master updated (59022ff -> 3a1a435)

[Andreas Tille]

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tille pushed a change to branch master
in repository physamp.

      from  59022ff   Upload to new
       new  5639c6d   d/watch pointing to Github
       new  1e8ed3d   Fix homepage
       new  d50a940   New upstream version 1.0.1
       new  58f58ae   Merge tag 'upstream/1.0.1'
       new  6964d64   New upstream version
       new  c6f1e62   debhelper 10
       new  3a1a435   Adjust versioned Build-Depends

The 7 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 +
 debian/changelog                         |   10 +
 debian/compat                            |    2 +-
 debian/control                           |    6 +-
 debian/copyright                         |    2 +-
 debian/watch                             |    4 +-
 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 ++++
 26 files changed, 2694 insertions(+), 247 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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