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Commits on May 29, 2018

• added imrpoved error checking in parser

  stamatak

  committedMay 29, 2018
  e700750

Commits on Jun 28, 2017

• fixed tree output in IC computation with partial gene trees

  stamatak

  committedJun 28, 2017
  197c7c5

Commits on Mar 10, 2017

• create new tagged release incorporating minor fixes

  stamatak

  committedMar 10, 2017
  9f786d6

Commits on Jul 20, 2016

• added flag: --print-identical-sequences that will tell RAxML to remove undetermined columns in the .reduced MSA file,

  stamatak

  committedJul 20, 2016
  e3641a5

Commits on Mar 23, 2016

• integrated Sarah's code for randomly subsampling quartets without replacement.

  stamatak

  committedMar 23, 2016
  a3d3006

Commits on Mar 10, 2016

• -added more verbose tree parser error messages for multi-furcating trees that will help to easily fix ill-formatted trees with

  stamatak

  committedMar 10, 2016
  acfd2ac

Commits on Feb 26, 2016

• 1. changed BS replicate generation option -f j to refuse generating BS replicates if original alignment contains completely undetermined columns

  stamatak

  committedFeb 26, 2016
  f5d0d44

Commits on Feb 24, 2016

• updated BS replicate generation to also generate correct bootstrap partition files.

  stamatak

  committedFeb 24, 2016
  640b68a

Commits on Oct 2, 2015

• fixed two bugs:

  stamatak

  committedOct 2, 2015
  9ab50c4

Commits on Aug 12, 2015

• 1. Integrated fallback for BFGS optimization to Brent-based optimization in case BFGS requires too many parameters.

  stamatak

  committedAug 12, 2015
  70c66a0

Commits on Aug 6, 2015

• updated axml.h

  stamatak

  committedAug 6, 2015
  a9b2aa2

• -changed optimization procedure for LG4X

  stamatak

  committedAug 6, 2015
  5439677

Commits on Aug 5, 2015

• cleaned up the code

  stamatak

  committedAug 5, 2015
  0468ca3

• fixed numerical problem in BFGS optimization

  stamatak

  committedAug 5, 2015
  9a02452

Commits on Jul 9, 2015

• added Kassian's code for TC/IC score calculations on partial gene trees

  stamatak

  committedJul 9, 2015
  8aeb9a9

Commits on Jun 29, 2015

• Fixed bug that made an assertion fail with the -M option

  stamatak

  committedJun 29, 2015
  852d2a5

Commits on Jun 25, 2015

• fixed major bug in likelihood functions for partitioned analyses with linked branch lengths

  stamatak

  committedJun 25, 2015
  e7c990d

Commits on Jun 15, 2015

• added option --set-thread-affinity to enable thread pinning for the hybrid MPI/PThreads version

  stamatak

  committedJun 15, 2015
  e3b3d01

Commits on May 21, 2015

• -fixed bug in BFGS optimization

  stamatak

  committedMay 21, 2015
  297bc55

Commits on Apr 18, 2015

• minor bug fixes

  stamatak

  committedApr 18, 2015
  b9048ea

Commits on Apr 15, 2015

• -added flags for computing JC69 and K80 DNA models

  stamatak

  committedApr 15, 2015
  40670a5

Commits on Apr 10, 2015

• -added ancestral state computation for LG4X and LG4M models

  stamatak

  committedApr 10, 2015
  411e39b

Commits on Feb 8, 2015

• added expliciit offendimng site printout for invariable sites that are in partitions that

  stamatak

  committedFeb 8, 2015
  cb84ec2

Commits on Jan 19, 2015

• When not specifying the number of threads via -T in the PThreads option, RAxML will now set

  stamatak

  committedJan 19, 2015
  53e5f18

Commits on Dec 27, 2014

• added new protein subst model stmtREV, see: http://datadryad.org/resource/doi:10.5061/dryad.7b470

  stamatak

  committedDec 27, 2014
  31501e7

Commits on Dec 19, 2014

• -added some additional error checking for partitions and the EPA algorithm, to prevent users

  stamatak

  committedDec 19, 2014
  52d3f18

Commits on Dec 16, 2014

• fixed a bug in lewis correction for asc. bias

  stamatak

  committedDec 16, 2014
  9706247

Commits on Dec 12, 2014

• fixed a bug in lewis ascertainment bias correction, the likelihoods were not correctly scaled in evaluateGeneric()

  stamatak

  committedDec 12, 2014
  97a901d

Commits on Dec 10, 2014

• fixed some issues with undetermined sites supression

  stamatak

  committedDec 10, 2014
  0816615

• added functionality to automatically remove fully undetermined sites from the alignment

  stamatak

  committedDec 10, 2014
  13a6f4c

Commits on Dec 5, 2014

• fixed a bug in the parser

  stamatak

  committedDec 5, 2014
  fe7c8a9

• update version numbers

  stamatak

  committedDec 5, 2014
  427762d

• updated manual

  stamatak

  committedDec 5, 2014
  3e0e1f5

Commits on Nov 28, 2014

• -added two additional ways for correcting ascertainment bias. Both new methods

  stamatak

  committedNov 28, 2014
  f3ea3d6

Commits on Nov 26, 2014

• fixed a bug in the Pthreads version of the evolutionary placement algorithm (EPA) that occured under the CAT model.

  stamatak

  committedNov 26, 2014
  5a695ce

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