Commits · aggr · phylo / fastcodeml

Browse files

Dec 03, 2015
- report number unique site for aggregation, not total · 26f929ff
  Iakov Davydov authored Dec 3, 2015
  
  26f929ff
- fix formatting · 8fb1fe23
  Iakov Davydov authored Dec 3, 2015
  
  8fb1fe23
- output number of aggregated codons only in verbose mode · 37455634
  Iakov Davydov authored Dec 3, 2015
  
  37455634
- output aggregation mode · 7b8dafb6
  Iakov Davydov authored Dec 3, 2015
  
  7b8dafb6
- remove nthreads message, thread number otputed twice · 8d80f461
  Iakov Davydov authored Dec 3, 2015
  
  8d80f461
- fix nthreads output (correct indentations) · 1124a669
  Iakov Davydov authored Dec 3, 2015
  
  1124a669
- retrive protoptype for the setLeaveProb & fix formatting · 73bd9b83
  Iakov Davydov authored Dec 3, 2015
  
  73bd9b83
- formatting from a7c7aee6 · 8386c1b1
  Iakov Davydov authored Dec 3, 2015
  
  8386c1b1
- fix multiple angular brackets and some comments formatting · 4aa62608
  Iakov Davydov authored Dec 3, 2015
  
  4aa62608
- fix angular braces in the style file · 0596cc46
  Iakov Davydov authored Dec 3, 2015
  
  0596cc46
- fix format.sh to not format nlopt.h · 1e15dfca
  Iakov Davydov authored Dec 3, 2015
  
  1e15dfca
- format all the code & revert simpleopt (broken in 2589ab and c3d6fe) · f540ad6d
  Iakov Davydov authored Dec 3, 2015
  
  f540ad6d
- code formatting scripts · 2b2b3cf9
  Iakov Davydov authored Dec 3, 2015
  
  2b2b3cf9
- only create mMapCodonPairToDistance if aggregation is used · 1e48dec6
  Iakov Davydov authored Dec 3, 2015
  
  1e48dec6
- aggregate=2, remove 3-codon distance · eeb311dd
  Iakov Davydov authored Dec 3, 2015
  
  eeb311dd
- find maximum minimal edit distance for s codon vector · 323f7586
  Iakov Davydov authored Dec 3, 2015
  
  323f7586
- create codon pair distance map · b6c6957f
  Iakov Davydov authored Dec 3, 2015
  
  b6c6957f
Dec 02, 2015
- re-enable tree reuse (it is disabled when aggregation is on) · a6b79a11
  Iakov Davydov authored Dec 2, 2015
  
  a6b79a11
- make aggregation a runtime option · a57fc232
  Iakov Davydov authored Dec 2, 2015
  
  a57fc232
Oct 16, 2015
- add fast_te: extract tree in fastcodeml format · e8a23100
  Iakov Davydov authored Oct 16, 2015
  
  e8a23100
Oct 15, 2015
- ensure that aggregation isn't used with lapack · 05e816c1
  Iakov Davydov authored Oct 15, 2015
  
  05e816c1
- disable tree reuse (it's not clear how to use it with aggregation) · 0ab09272
  Iakov Davydov authored Oct 15, 2015
  
  0ab09272
Jun 17, 2015
- fix frequency multiplication for unobserved state · 951552b7
  Iakov Davydov authored Jun 17, 2015
  
  951552b7
Jun 16, 2015
- proper likelihood computation for ambigous states · f43a1bad
  Iakov Davydov authored Jun 16, 2015
  
  f43a1bad
May 16, 2015
- fast_cont.py utility to proceed computation from aggregated point · 3652b21b
  Iakov Davydov authored May 16, 2015
  
  3652b21b
- fix issue \!16 (output broken), also remove extra tab in output · b9acef4a
  Iakov Davydov authored May 16, 2015
  
  b9acef4a
Mar 26, 2015
- state aggregation for observed states · b77789cd
  Iakov Davydov authored Mar 26, 2015
  
  b77789cd
- ignore some files in git · 97e5dca5
  Iakov Davydov authored Mar 26, 2015
  
  97e5dca5
- remove trailing spaces from .cpp and .h files · c3d6fe8a
  Iakov Davydov authored Mar 26, 2015
  
  c3d6fe8a
- spaces to tabs · 2589ab54
  Iakov Davydov authored Mar 26, 2015
  
  2589ab54
- dos2unix all files · 5e1e24c9
  Iakov Davydov authored Mar 26, 2015
  
  5e1e24c9
Sep 04, 2014
- · df73db35
  smoretti authored Sep 4, 2014
  df73db35
Jun 27, 2014
- 1.2.0 - BG/Q compatibility (V.Keller, K.Ali) · 4b0557fe
  kali authored Jun 27, 2014
  4b0557fe
Jun 16, 2014
- · e1013ebc
  smoretti authored Jun 16, 2014
  e1013ebc
Apr 07, 2014
- · 49a94d91
  smoretti authored Apr 7, 2014
  49a94d91
Mar 27, 2014
- -np (no paraller) readded · 5a383e68
  akalantz authored Mar 27, 2014
  5a383e68
Mar 26, 2014
- Update Alexandra's WriteResults.cpp · 316fbebc
  smoretti authored Mar 26, 2014
  316fbebc
Mar 25, 2014
- Extend INSTALL file · 649e9783
  smoretti authored Mar 25, 2014
  649e9783
Mar 18, 2014
- · abba19cc
  smoretti authored Mar 18, 2014
  abba19cc
- Add TODO file · 2b933d99
  smoretti authored Mar 18, 2014
  2b933d99