Commits · 9ec41ac41712996963f7b10ebaa8fe43bf32daae · phylo / fastcodeml

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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
- Implemented CPV scaling · 74cadc80
  mvalle authored Feb 7, 2013
  74cadc80
Feb 05, 2013
- Removed global scaling code · 53d56791
  mvalle authored Feb 5, 2013
  53d56791
- Added guard against infinites in results · 22133b10
  mvalle authored Feb 5, 2013
  22133b10
Feb 01, 2013
- Different seed for different MPI processes. · 177d77f5
  mvalle authored Feb 1, 2013
  177d77f5
Jan 28, 2013
- Changed variable initialization logic. · fa0dfd72
  mvalle authored Jan 28, 2013
  fa0dfd72
Jan 24, 2013
- Fixed doxygen comments. · c99c26c9
  mvalle authored Jan 24, 2013
  c99c26c9
- Fixed various typos in doxygen comments and in two exception messages. · 94715e19
  mvalle authored Jan 24, 2013
  94715e19
- Updated doxygen to 1.8.3.1 · 0d0f30a0
  mvalle authored Jan 24, 2013
  0d0f30a0
Jan 18, 2013
- Minor improvements to code and comments · 38c02be3
  mvalle authored Jan 18, 2013
  38c02be3
Jan 17, 2013
- Corrected gap/ambiguous positions discovery. · 87e32b97
  mvalle authored Jan 17, 2013
  87e32b97
Jan 15, 2013
- · ec3a20ec
  hschabau authored Jan 15, 2013
  ec3a20ec
- Fixed read for specific msa (specie name alone on a line) · 736673e2
  mvalle authored Jan 15, 2013
  736673e2
Jan 14, 2013
- Restricted Doxygen to *.h and *.cpp files · 58c7c0a0
  mvalle authored Jan 14, 2013
  58c7c0a0
Jan 11, 2013
- Fixed Doxyfile. Fixed Doxygen comment in source. · 20c6890a
  mvalle authored Jan 11, 2013
  20c6890a
- Corrected comment · f509e265
  mvalle authored Jan 11, 2013
  f509e265
- Added check for no internal branches · 88257242
  mvalle authored Jan 11, 2013
  88257242
Jan 10, 2013
- Removed commented code · a8f82c78
  mvalle authored Jan 10, 2013
  a8f82c78
Jan 08, 2013
- Print and remove gaps. Print num of ambiguous sites · 00b3dbc0
  mvalle authored Jan 8, 2013
  00b3dbc0
Jan 07, 2013
- cleaning up · 86c0668f
  hschabau authored Jan 7, 2013
  86c0668f
- Changed LRT print format for MPI · d829690e
  mvalle authored Jan 7, 2013
  d829690e
Jan 02, 2013
- Added variable print also for MPI · f8586a87
  mvalle authored Jan 2, 2013
  f8586a87
Dec 28, 2012
- Remove spaces from newick tree before parsing (the parser cannot cope with them) · f25a92bd
  mvalle authored Dec 28, 2012
  f25a92bd
Dec 24, 2012
- On ambiguous codons initialize leaves to 1/n_codons · 84ebf573
  mvalle authored Dec 24, 2012
  84ebf573