Release Notes

Version 2.3:
  • [2.3.0] - 04-29-2014
  • [2.3.1] - 04-30-2014
  • [2.3.2] - 05-08-2014
  • [2.3.3] - 05-11-2014
  • [2.3.4] - 05-24-2014
  • [2.3.5] - 09-09-2014
  • [2.3.6] - 03-26-2015
  • [2.3.7] - 06-15-2015
  • [2.3.8] - 01-30-2016
  • Speed
    • [0-100% faster] Rewrite new model framework.
    • [2.3.2] - Resample letter frequencies more, but not too much.
    • [2.3.3] [30% faster] Don't recalculate likelihoods unless necessary.
    • [2.3.4] [0-25% faster] Work with large trees more efficiently.
    • [2.3.4] [0-100% faster] Compute likelihoods on ambiguous sequences better.
    • [2.3.6] [0-50% faster] Speed improvements for graphical models.
    • [2.3.8] [~10% faster] More efficient object representation.
  • Models
    • [2.3.5] - Enable generic models written as Haskell.
    • [2.3.3] - Fix and enable M1a, M2a, M2a_Test, M7, M8, M8a, M8a_Test.
    • [2.3.5] - Fix crashes with gamma and log-normal rate variation
    • [2.3.5] - Fix parsing of frequency models like "+F" in LG+F+gamma_inv
    • [2.3.6] - Add M3 and M3_Test.
  • Internals
    • Rewrite alignment MCMC
  • Input
    • [2.3.4] Handle ambiguous nucleotides K, B, D, M, H, and V in nucleotide and codon alphabets.
  • Summarization tools
    • bp-analyze.pl - Generate prettier HTML reports.
    • bp-analyze.pl - Log all sub-commands.
    • bp-analyze.pl - Handle /cygdrive/ on cygwin.
    • [2.3.2] bp-analyze.pl - Correctly handle not having R.
    • [2.3.2] - Update alignment diffs to be more useful.
    • [2.3.6] statreport - Allow reporting posterior mode.
    • [2.3.6] statreport - Report HPD credible intervals.
  • Changes
    • Replace 'meanIndelLengthminusOne' with 'meanIndelLength'
    • [2.3.6] - Change --show-only option to --test.
  • Fixes
    • [2.3.8] Stop crashing on gamma[n] models.

comments and suggestions: benjamin . redelings * gmail + com