Commits · fa0dfd7235bb0c214c4e2ffd7a18ea99a4218a6c · phylo / fastcodeml

Browse files

Jan 28, 2013
- Changed variable initialization logic. · fa0dfd72
  mvalle authored Jan 28, 2013
  fa0dfd72
Jan 24, 2013
- 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 15, 2013
- 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
Dec 21, 2012
- Moved to main the check for null branch lengths from file. · da40b5aa
  mvalle authored Dec 21, 2012
  da40b5aa
Dec 19, 2012
- Print annotated tree with the internal branch number. · 82d4e2bc
  mvalle authored Dec 19, 2012
  82d4e2bc
- Added print of the LRT value · 9d0d0871
  mvalle authored Dec 19, 2012
  9d0d0871
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 06, 2012
- Restructured few error messages. · 064a0a48
  mvalle authored Dec 6, 2012
  064a0a48
- Added print num internal branches · 40acf8ea
  mvalle authored Dec 6, 2012
  40acf8ea
Dec 04, 2012
- Added print parameters. · a1a6de2f
  mvalle authored Dec 4, 2012
  a1a6de2f
Dec 03, 2012
- Fixed bug that appears in beb only using -nr flag. · 2d27a5b2
  mvalle authored Dec 3, 2012
  2d27a5b2
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
Nov 18, 2012
- Help message correction · 22fa4bd1
  mvalle authored Nov 18, 2012
  22fa4bd1
- Added option -ps --no-pre-stop Don't stop H0 maximization if it cannot satisfy LRT (default: stop) · 5f1d3656
  mvalle authored Nov 18, 2012
  5f1d3656
Nov 09, 2012
- Removed variables used in testing, added printout arguments for a XMT compilation problem · 11012557
  mvalle authored Nov 9, 2012
  11012557
Nov 06, 2012
- Added support for ambiguous codons. · d1d7c9b6
  mvalle authored Nov 6, 2012
  d1d7c9b6
Oct 29, 2012
- Added mapping sites to original number · 85489f15
  mvalle authored Oct 29, 2012
  85489f15
Oct 25, 2012
- Refactory changes (especially in Ming2) · ead0e2ec
  mvalle authored Oct 25, 2012
  ead0e2ec
Oct 18, 2012
- Added check for zero valid sites · 8ce34773
  mvalle authored Oct 18, 2012
  8ce34773
Oct 14, 2012
- Added exception for bad_alloc · 8fb3a6c0
  mvalle authored Oct 14, 2012
  8fb3a6c0
Oct 12, 2012
- Code restructuring · 6856879a
  mvalle authored Oct 12, 2012
  6856879a
Oct 10, 2012
- Finished fixing MPI for BEB. · 5e5adff6
  mvalle authored Oct 10, 2012
  5e5adff6
- Added more code for BEB · f26764f5
  mvalle authored Oct 10, 2012
  f26764f5
Oct 09, 2012
- Cleared unused or moved code. · 038bec91
  mvalle authored Oct 9, 2012
  038bec91
Oct 02, 2012
- As default the multiplication with codon frequencies has been moved up one level · bdbb5567
  mvalle authored Oct 2, 2012
  bdbb5567
Sep 25, 2012
- Fixed various doxygen comments and the Doxyfile parameters to comment all parts of the code · 5dc4c022
  mvalle authored Sep 25, 2012
  5dc4c022
Sep 24, 2012
- Corrected bad error handling for MPI initialization · e42eeedc
  mvalle authored Sep 24, 2012
  e42eeedc
Sep 14, 2012
- Comment corrections. · f5745dae
  mvalle authored Sep 14, 2012
  f5745dae
- Added option and code to apply subtree reuse to blocks instead to the full set of sites. · 9aee26c9
  mvalle authored Sep 14, 2012
  9aee26c9
Sep 11, 2012
- Added OpenMP TASK use · 7017caa7
  mvalle authored Sep 11, 2012
  7017caa7
Sep 10, 2012
- Split Srobability matrix class in two (one for each hypothesis) · ccae1609
  mvalle authored Sep 10, 2012
  ccae1609
Sep 04, 2012
- Reduced size few ForestNode variables · 4f0d3f08
  mvalle authored Sep 4, 2012
  4f0d3f08