Commits · a8f4ae3efab93cea48fe6c90cc61b83a4b09154d · phylo / fastcodeml

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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
Dec 21, 2012
- Moved to main the check for null branch lengths from file. · da40b5aa
  mvalle authored Dec 21, 2012
  da40b5aa
Dec 19, 2012
- Corrected message silencing for MPI version. · 8d4fe618
  mvalle authored Dec 19, 2012
  8d4fe618
- Print annotated tree with the internal branch number. · 82d4e2bc
  mvalle authored Dec 19, 2012
  82d4e2bc
- Fixed messages from MPI execution. · 3b7e20cb
  mvalle authored Dec 19, 2012
  3b7e20cb
- Added print of the LRT value · 9d0d0871
  mvalle authored Dec 19, 2012
  9d0d0871
Dec 18, 2012
- · ee1c914d
  hschabau authored Dec 18, 2012
  ee1c914d
Dec 15, 2012
- Ordered output sites under positive selection. · 5471b672
  mvalle authored Dec 15, 2012
  5471b672
Dec 13, 2012
- Changed option --times-from-file to --lenghts-from-file · dd310797
  mvalle authored Dec 13, 2012
  dd310797
Dec 12, 2012
- Changed message output to cout from cerr. · ee5c527a
  mvalle authored Dec 12, 2012
  ee5c527a
Dec 11, 2012
- Fixed problem with ambiguous codons. · ad0c251f
  mvalle authored Dec 11, 2012
  ad0c251f
- added paths for dev · 67cb81bc
  hschabau authored Dec 11, 2012
  67cb81bc
Dec 06, 2012
- Changed output of sites under positive selection so the site number starts from 1 and not zero. · a021808c
  mvalle authored Dec 6, 2012
  a021808c