Commits · 0d0f30a034acf487d02eba39427bdcc3d8f02ab8 · phylo / fastcodeml

Browse files

Jan 24, 2013
- 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
- Restructured few error messages. · 064a0a48
  mvalle authored Dec 6, 2012
  064a0a48
- Added print num internal branches · 40acf8ea
  mvalle authored Dec 6, 2012
  40acf8ea
Dec 05, 2012
- · 98bf503e
  hschabau authored Dec 5, 2012
  98bf503e
- · af416431
  hschabau authored Dec 5, 2012
  af416431
Dec 04, 2012
- Added print parameters. · a1a6de2f
  mvalle authored Dec 4, 2012
  a1a6de2f
- Changed variable name conflicting with reserved word · 6ca0ee3e
  mvalle authored Dec 4, 2012
  6ca0ee3e
- Changed newick grammar to accept species names starting with number. · 7b82e33e
  mvalle authored Dec 4, 2012
  7b82e33e
Dec 03, 2012
- Fixed bug that appears in beb only using -nr flag. · 2d27a5b2
  mvalle authored Dec 3, 2012
  2d27a5b2
Dec 01, 2012
- generated mpi version for castor · 31f394a2
  hschabau authored Dec 1, 2012
  31f394a2
Nov 30, 2012
- Fixed CMAKE_SKIP_RPATH for XMT · baf00e10
  mvalle authored Nov 30, 2012
  baf00e10
Nov 28, 2012
- Removed commented out test code (still BEB test code is still in place) · 357871ad
  mvalle authored Nov 28, 2012
  357871ad
Nov 24, 2012
- Removed testing code · 0b424b4e
  mvalle authored Nov 24, 2012
  0b424b4e