Commits · 3b60da8ff8ede26e4106f2dc4a1fd6f30ae70a63 · phylo / fastcodeml

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Jan 23, 2014
- branch lenghts fixed attribute added (-bl) · 3b60da8f
  akalantz authored Jan 23, 2014
  3b60da8f
Jan 21, 2014
- Put rooted and unrooted tree for the README example · 1d5901d3
  smoretti authored Jan 21, 2014
  1d5901d3
- warning message for unrooted tree and codeML algorithm is set as the default one · 9fafe16c
  akalantz authored Jan 21, 2014
  9fafe16c
Dec 20, 2013
- Cleaning · 53093a0b
  smoretti authored Dec 20, 2013
  53093a0b
- · 19acdeec
  smoretti authored Dec 20, 2013
  19acdeec
- · 92ead07f
  smoretti authored Dec 20, 2013
  92ead07f
Dec 17, 2013
- Add nlopt.h · 8e7f1624
  akalantz authored Dec 17, 2013
  8e7f1624
- Add number_threads + change output file · 94b0ddc0
  akalantz authored Dec 17, 2013
  94b0ddc0
Dec 16, 2013
- Add the unrooted tree (unrooted by NewickUtilities) as example because branch... · 6a05a0a8
  smoretti authored Dec 16, 2013
  6a05a0a8
- Add the README file from the package + basic example files · aad6fb95
  smoretti authored Dec 16, 2013
  aad6fb95
- Rename former README as INSTALL · 8d9e0628
  smoretti authored Dec 16, 2013
  8d9e0628
Jul 02, 2013
- cleaning up · 44f69dc4
  hschabau authored Jul 2, 2013
  44f69dc4
Jun 20, 2013
- finishing fastcodeml paper submission · e215432f
  hschabau authored Jun 20, 2013
  e215432f
Jun 04, 2013
- · 0674fa2e
  hschabau authored Jun 4, 2013
  0674fa2e
May 29, 2013
- Added exception for LRT not satisfied. · 64f47277
  mvalle authored May 29, 2013
  64f47277
May 15, 2013
- added epflcpt15 installation settings · 9bd7b64a
  hschabau authored May 15, 2013
  9bd7b64a
- Clarified comments. · 3f15b4e8
  mvalle authored May 15, 2013
  3f15b4e8
Apr 30, 2013
- Added comments. Cleaned few datatypes · c96fbb3d
  mvalle authored Apr 30, 2013
  c96fbb3d
- Changed exception that ends optimization in the event of LRT not satisfied · 1657c884
  mvalle authored Apr 30, 2013
  1657c884
Apr 26, 2013
- Fixed print bug in m22. · d2d46ac2
  mvalle authored Apr 26, 2013
  d2d46ac2
- fixed cut and paste error · 34f46eff
  mvalle authored Apr 26, 2013
  34f46eff
- Renamed constant to reflect the program logic · c4ac4001
  mvalle authored Apr 26, 2013
  c4ac4001
- Changed initialization of variables to be like it is done in CodeML. · bbd7141e
  mvalle authored Apr 26, 2013
  bbd7141e
Apr 25, 2013
- Added codon frequency table print connected to the verbose value. · 9ec41ac4
  mvalle authored Apr 25, 2013
  9ec41ac4
Apr 24, 2013
- Fixed codon frequencies calculation for ambiguous codons · 7c30fd34
  mvalle authored Apr 24, 2013
  7c30fd34
Apr 23, 2013
- Unify codon frequencies print format with CodeML, start attaching ambiguous... · cf964c42
  mvalle authored Apr 23, 2013
  cf964c42
Apr 22, 2013
- Removed printing of codon empirical frequencies · 587f1e08
  mvalle authored Apr 22, 2013
  587f1e08
- Fixed case with codon frequencies equal zero · bf00228f
  mvalle authored Apr 22, 2013
  bf00228f
Apr 16, 2013
- Implemented codon frequency estimation for ambiguous data as in CodeML · 9df18794
  mvalle authored Apr 16, 2013
  9df18794
- Added compile option for totally ambiguous codon all one · c96acc3d
  mvalle authored Apr 16, 2013
  c96acc3d
Apr 10, 2013
- Added LRT optimization also to m22 optimizer · a8cdde25
  mvalle authored Apr 10, 2013
  a8cdde25
Apr 09, 2013
- update · 562b86a1
  hschabau authored Apr 9, 2013
  562b86a1
- update · 3ff0b352
  hschabau authored Apr 9, 2013
  3ff0b352
- Fixed race condition if MSA file malformed · 80e9112e
  mvalle authored Apr 9, 2013
  80e9112e
Feb 22, 2013
- Removed dead test code · 9e38f089
  mvalle authored Feb 22, 2013
  9e38f089
Feb 20, 2013
- Added hyp selection also for MPI jobs · a8f4ae3e
  mvalle authored Feb 20, 2013
  a8f4ae3e
Feb 14, 2013
- added first FastCodeML spec file for Vital-IT RPM generation · 5bc80a74
  hstockin authored Feb 14, 2013
  5bc80a74
- Added immediate check on the optimizer code. · 363e5706
  mvalle authored Feb 14, 2013
  363e5706
Feb 07, 2013
- Fixed doxyfile with the new cpv scaling · c96c93c7
  mvalle authored Feb 7, 2013
  c96c93c7
- Fixed cpv scalind for new likelihood · 4e5b7063
  mvalle authored Feb 7, 2013
  4e5b7063