Commits · ee5c527a84779997e3f871575402ea2d1cbd93e4 · phylo / fastcodeml

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Dec 12, 2012
- Changed message output to cout from cerr. · ee5c527a
  mvalle authored Dec 12, 2012
  ee5c527a
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 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 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 02, 2012
- As default the multiplication with codon frequencies has been moved up one level · bdbb5567
  mvalle authored Oct 2, 2012
  bdbb5567
Sep 24, 2012
- Corrected bad error handling for MPI initialization · e42eeedc
  mvalle authored Sep 24, 2012
  e42eeedc
Sep 14, 2012
- Added option and code to apply subtree reuse to blocks instead to the full set of sites. · 9aee26c9
  mvalle authored Sep 14, 2012
  9aee26c9
Aug 23, 2012
- Remove command line options related to MKL. · a8a9b564
  mvalle authored Aug 23, 2012
  a8a9b564
- Small improvements to reduce warnings from compilers · b26f4d29
  mvalle authored Aug 23, 2012
  b26f4d29
Aug 21, 2012
- Fixed omp schedule · 79a3b48f
  mvalle authored Aug 21, 2012
  79a3b48f
Jul 03, 2012
- Added option to set relative error on lnl as stopping criteria. · 49cbf98c
  mvalle authored Jul 3, 2012
  49cbf98c
Jun 19, 2012
- Added -x option to enable printing intermediate lnl. · 6b099d31
  mvalle authored Jun 19, 2012
  6b099d31
Apr 11, 2012
- Fixed comments · 3a3751aa
  mvalle authored Apr 11, 2012
  3a3751aa
Apr 02, 2012
- Fixed warning for Win 64 bits compilation. · 4622832d
  mvalle authored Apr 2, 2012
  4622832d
Feb 28, 2012
- New exception message formatting using ostringstream. · 2fa03b93
  mvalle authored Feb 28, 2012
  2fa03b93
Feb 21, 2012
- Reorganized options to initialize values. · 98efd3eb
  mvalle authored Feb 21, 2012
  98efd3eb
- Added setting of initial values from the command line · ce3d4f66
  mvalle authored Feb 21, 2012
  ce3d4f66
- Fixed doxygen comments · 63c6a6f7
  mvalle authored Feb 21, 2012
  63c6a6f7
- Added option -p for minimal initialization for testing (p0=1 the other proportions set to zero) · 4b1b5557
  mvalle authored Feb 21, 2012
  4b1b5557
Feb 03, 2012
- Updated Doxygen comments · 3125cfd1
  mvalle authored Feb 3, 2012
  3125cfd1
Feb 02, 2012
- Removed no-aggressive option (so the reduction is always aggressive). Removed... · 41e60292
  mvalle authored Feb 2, 2012
  41e60292
Jan 11, 2012
- Fixed help on the CodeML optimizer · 9915b78e
  mvalle authored Jan 11, 2012
  9915b78e
Jan 09, 2012
- Fixed doxygen comments. · cd41d84b
  mvalle authored Jan 9, 2012
  cd41d84b
Dec 23, 2011
- Reorganized optimization initialization. · fc8c2692
  mvalle authored Dec 23, 2011
  fc8c2692
Dec 20, 2011
- Added new optimization algorithms · ecf0e03a
  mvalle authored Dec 20, 2011
  ecf0e03a
Dec 16, 2011
- Fixed various Doxygen comments · 534595da
  mvalle authored Dec 16, 2011
  534595da
Dec 13, 2011
- Rationalized variable printing. · f4d5bce1
  mvalle authored Dec 13, 2011
  f4d5bce1
Nov 15, 2011
- Added NoTipPruning testing option. · 62e9d2b1
  mvalle authored Nov 15, 2011
  62e9d2b1
Nov 04, 2011
- More 'const' usage · 6a6ee9b7
  mvalle authored Nov 4, 2011
  6a6ee9b7
Oct 28, 2011
- Added alignment on a cache line also to the new likelihood method. · 249d7b23
  mvalle authored Oct 28, 2011
  249d7b23
Oct 18, 2011
- Used vector of bool for mGoodCodon. Added safeguard against negative... · 34df0702
  mvalle authored Oct 18, 2011
  34df0702
Oct 04, 2011
- Coding style fixes · 142a4fab
  mvalle authored Oct 4, 2011
  142a4fab
Sep 28, 2011
- Clarified variable names (difference branch/node), added option to select... · 8ef130a5
  mvalle authored Sep 28, 2011
  8ef130a5
May 30, 2011
- Added option to compute only one hypothesis · 9ad17fa7
  mvalle authored May 30, 2011
  9ad17fa7
May 06, 2011
- · c080a219
  hschabau authored May 6, 2011
  c080a219