Release Notes

Version 2.1.1 (02/03/11)

Version 2.1.1 fixes bugs and is easier to use.

  • Bug fixes
    • Fixed: 2.1.0 would sometimes crash randomly during long runs.
    • Fixed: Windows binaries used the same random seed every time.
    • Fixed: Broken M0 and M7 model priors.
  • Usability
    • Read files in old macintosh format on UNIX and Windows.
  • Build
    • Fix build from source with system BOOST libraries.

Version 2.1.0 (07/07/10)

Version 2.1.0 adds some major new features:

  • Major new features.
    1. Allow multiple separate genes (i.e. data partitions).
      • The alignment of each gene may be either fixed or variable.
    2. Improve mixing when the tree has many tips (for MCMC)
    3. Improve initial search when the tree has many tips (for estimation)
    4. Use much less RAM.
  • MCMC Speed and reliability
    • Use slice sampling for continous parameters -- automatically detect step-size.
    • Allow SPR moves to intelligently propose attachment sites.
    • Improve CPU efficiency when the alignment is constrained.
    • Spend more time resampling topology and alignment, versus substitution parameters.
  • Models
    • Default to more conservative gamma prior for branch lengths.
    • New substitution models: C10 and C20.
  • Usability
    • Stop requiring --data-dir option: the information is now internal.
    • Handle amino-acid code J.
    • Warn on illegal characters.
    • New analysis script replaces GNUmakefile.
  • Summarization tools
    • Report the maximum posterior decoding alignment.
    • Simplify computing the consensus tree and other summaries.
    • Check mixing and effective sample sizes by comparing multiple runs.

comments and suggestions: benjamin . redelings * gmail + com