[med-svn] [physamp] branch upstream updated (d50a940 -> ce05445)

[Julien Dutheil]

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jdutheil-guest pushed a change to branch upstream
in repository physamp.

      from  d50a940   New upstream version 1.0.1
      adds  64fac36   First version of bppalnoptim.
      adds  3e9fa13   Added cmake files in doc and man.
      adds  2b71ea8   Initial fix for standalone version.
      adds  7974664   Ouput of filtered sequences is now optional.
      adds  b30d9e7   Added license files (GPL3).
      adds  750a1c4   Added man pages.
      adds  6285e23   Added first draft of manual + example files.
      adds  5806000   Release 0.1.0.
      adds  e6565f2   Fixed dir name.
      adds  0f09f72   Automatic arch.
      adds  b4570b5   Added new stop criterion (nb sites). Memory required for distance matrix is also shown.
      adds  fa922ab   Modifs for revision.
      adds  dc04ac1   Documentation updated.
      adds  f6f81d5   Fixed dist version nb.
      adds  35dbd17   Added ChangeLog
      adds  804d620   Version 0.2.0.
      adds  c3c87eb   Merge branch 'master' of biopp.univ-montp2.fr:/git/physamp
      adds  51ad435   Added example file for bppphysamp.
      adds  39feaed   Compatibility update
      adds  a55bf2c   Added bppPhySamp.
      adds  dbd0466   Initial commit
      adds  b481396   Merge branch 'master' of https://github.com/jydu/physamp
      adds  1d59ff2   Fixed man pages.
      adds  3642f5c   Set theme jekyll-theme-time-machine
      adds  7effeb6   Create physamp.md
      adds  d4734bb   Merge branch 'master' of https://github.com/jydu/physamp
      adds  065606b   Moved all documents from doc to docs.
      adds  186574e   Renamed index page.
      adds  bdba536   Update index.md
      adds  6bb6597   Update index.md
      adds  cb31b2e   Set theme jekyll-theme-slate
      adds  5c86027   Update index.md
      adds  8381096   Update index.md
      adds  a574878   Release 1.0.0.
      adds  ed52064   Merge branch 'master' of biopp.univ-montp2.fr:/git/physamp
      adds  5c5e523   Fixed spec file.
      adds  c38a030   Version 1.0.1.
      adds  5a52fb2   Fixed deprecated auto_ptr
      adds  8906dde   Merge branch 'master' of https://github.com/jydu/physamp into upstream
      adds  22859e0   Fixed CPAck version.
      adds  ce05445   Merge branch 'master' of https://github.com/jydu/physamp into upstream

No new revisions were added by this update.

Summary of changes:
 CMakeLists.txt                 |  4 ++--
 physamp/AlignmentOptimizer.cpp | 19 ++++++++++---------
 physamp/CMakeLists.txt         |  5 +++--
 physamp/PhyloSampler.cpp       |  4 ++--
 4 files changed, 17 insertions(+), 15 deletions(-)

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