Commits · fa0dfd7235bb0c214c4e2ffd7a18ea99a4218a6c · phylo / fastcodeml

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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
Dec 12, 2012
- Changed message output to cout from cerr. · ee5c527a
  mvalle authored Dec 12, 2012
  ee5c527a
Dec 04, 2012
- Added print parameters. · a1a6de2f
  mvalle authored Dec 4, 2012
  a1a6de2f
Nov 24, 2012
- Removed testing code · 0b424b4e
  mvalle authored Nov 24, 2012
  0b424b4e
Oct 18, 2012
- Added check for zero valid sites · 8ce34773
  mvalle authored Oct 18, 2012
  8ce34773
Oct 10, 2012
- 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 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
Aug 28, 2012
- Fixed Cmake problem if math lib present and not use_lapack · 9a85471a
  mvalle authored Aug 28, 2012
  9a85471a
Aug 21, 2012
- Fixed omp schedule · 79a3b48f
  mvalle authored Aug 21, 2012
  79a3b48f
Jul 12, 2012
- Added Vampir profiling support · baba849c
  mvalle authored Jul 12, 2012
  baba849c
Jul 03, 2012
- Added option to set relative error on lnl as stopping criteria. · 49cbf98c
  mvalle authored Jul 3, 2012
  49cbf98c
Jun 19, 2012
- Fixed Doxygen comments · de3ba105
  mvalle authored Jun 19, 2012
  de3ba105
- Added -x option to enable printing intermediate lnl. · 6b099d31
  mvalle authored Jun 19, 2012
  6b099d31
Apr 02, 2012
- Fixed warning for Win 64 bits compilation. · 4622832d
  mvalle authored Apr 2, 2012
  4622832d
Mar 26, 2012
- Fixed comments · 5336e315
  mvalle authored Mar 26, 2012
  5336e315
Feb 21, 2012
- Reorganized options to initialize values. · 98efd3eb
  mvalle authored Feb 21, 2012
  98efd3eb
- Added option -p for minimal initialization for testing (p0=1 the other proportions set to zero) · 4b1b5557
  mvalle authored Feb 21, 2012
  4b1b5557
- More efficient initialization of loops using iterators · 43dc07a7
  mvalle authored Feb 21, 2012
  43dc07a7
Feb 19, 2012
- Removed old-style casts · e9fa3d68
  mvalle authored Feb 19, 2012
  e9fa3d68
Feb 17, 2012
- Removed unneeded virtual function and changed to base class method · 722903bf
  mvalle authored Feb 17, 2012
  722903bf
Feb 15, 2012
- Simpified Forest interface · 8a9b9f2f
  mvalle authored Feb 15, 2012
  8a9b9f2f
- Added abstraction layer to insulate readers. · 869c7705
  mvalle authored Feb 15, 2012
  869c7705
Feb 13, 2012
- Extracted forest export functions as friend class · cad5057b
  mvalle authored Feb 13, 2012
  cad5057b
Feb 10, 2012
- Moved static parts out of inner loop in TransitionMatrixSet · 4a015ab2
  mvalle authored Feb 10, 2012
  4a015ab2
Jan 26, 2012
- Extract and print number of evaluations. · 8220b30f
  mvalle authored Jan 26, 2012
  8220b30f
Jan 11, 2012
- Added CodeML optimizer. · cef74b37
  mvalle authored Jan 11, 2012
  cef74b37
Jan 09, 2012
- Fixed doxygen comments. · cd41d84b
  mvalle authored Jan 9, 2012
  cd41d84b
Jan 02, 2012
- Cosmetic changes · 6e228b7e
  mvalle authored Jan 2, 2012
  6e228b7e
Dec 23, 2011
- Reorganized optimization initialization. · fc8c2692
  mvalle authored Dec 23, 2011
  fc8c2692
Dec 21, 2011
- Used everywhere elementWiseMult · a5ff2958
  mvalle authored Dec 21, 2011
  a5ff2958
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 18, 2011
- Changed oneCycleMaximizer to computeLikelihood (and for Forest computeLikelihoods) · e2216c28
  mvalle authored Nov 18, 2011
  e2216c28