Commits · 5471b672e9bac767dd61afb3da9962efe9ca6800 · phylo / fastcodeml

Browse files

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
Nov 22, 2012
- update · fb6151d2
  hschabau authored Nov 22, 2012
  fb6151d2
- update · c7c77395
  hschabau authored Nov 22, 2012
  c7c77395
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 15, 2012
- · 242dfbd1
  hschabau authored Nov 15, 2012
  242dfbd1
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
- Cleaning · c34560cb
  mvalle authored Oct 29, 2012
  c34560cb
Oct 25, 2012
- Refactory changes (especially in Ming2) · ead0e2ec
  mvalle authored Oct 25, 2012
  ead0e2ec
- · b7aa0327
  hschabau authored Oct 25, 2012
  b7aa0327
Oct 19, 2012
- Changed loading of std::map for efficiency. · 76ad1f34
  mvalle authored Oct 19, 2012
  76ad1f34
Oct 18, 2012
- Fixed bug in MPI results print · 331282bd
  mvalle authored Oct 18, 2012
  331282bd
- 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 11, 2012
- Removed vdExp usage that has problems with MPI · e5a7b966
  mvalle authored Oct 11, 2012
  e5a7b966
- Changed comments, added cast · 6a482168
  mvalle authored Oct 11, 2012
  6a482168
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
- · 398b4e71
  hschabau authored Oct 10, 2012
  398b4e71
Oct 09, 2012
- testing fastcodeml · d11ae9d0
  hschabau authored Oct 9, 2012
  d11ae9d0