Release Notes

Version 2.0.2 (02/03/09)

Version 2.0.2 fixes some bugs and updates the auxiliary tools to be more similar to the development version. It also has some speedups when the alignment is partially fixed (constrained).

  • General
    • Make alignment constraints work again.
    • Represent stop codons as "*" instead of "!".
  • Executables
    • Compile windows executables with an up-to-date compiler
  • Don't crash...
    • Don't crash in MCMC when using the gamma distribution. (really)
  • Useability
    • Capitalize model names WAG, PAM, JTT, etc.
    • Improve checks for illegal characters in sequence names.
    • Improve checks for illegal characters in alignment.
    • Generate correct colors for DNA AU plots
    • In case of errors in the post hoc analysis, give useful error messages.
  • Experimental...
    • alignment-align: align two alignments to compare them.
    • alignment-max: generate a representative alignment.

Version 2.0.1 (12/11/07)

Version 2.0.1 fixes several bugs. In order to ensure stability, no major features were added in this release.

This release fixes a bug that affected results in default gap model, and so we recommend that all users upgrade to this release. This bug previously resulted in under-estimates of the mean gap length.

  • Correctness
    • Fix sampling of the mean gap length (epsilon) under the (default) RS07 model.
  • Executables
    • Make Macintosh executables run correctly (static linkage)
  • Don't crash...
    • Don't crash in MCMC when changing branch lengths.
    • Don't crash in MCMC when using the gamma distribution.
    • Don't crash on --show-only.
    • Don't crash analyzing collection of FastA alignments.
  • Usability
    • Don't quit reading a FastA file on blank lines.
    • Generate better consensus alignment.
    • [configure] Correctly check for GSL version 1.8 of higher.
    • [configure] Don't blame GSL for bad compiler flags for cpu architecture.

Version 2.0.0 (08/10/07)

In version 2.0.0 I have added a few new features and fixed many bugs. I have made bali-phy much simpler and easier to use. Several new features and improvements are listed below:

  • Variables
    • Use Tracer to visualize MCMC runs.
    • Unified handling of variables including frequencies, mu (branch length mean), etc.
    • Variables can all be monitored with Tracer, and can be fixed.
  • Data
    • Use information in ambiguous letters (below).
    • Handle {R, Y, W, S} in codon alphabets.
    • Handle {B, Z} in amino acid alphabets.
    • Allow non-standard genetic codes.
  • New Substitution Models
    • GTR (nucleotides)
    • HKYx3 / TNx3 / GTRx3 (triplets)
    • rates ~ log-normal[n]
  • MCMC improvements
    • Topology constraints.
    • Fix the alignment along a branch.
    • Improve proposals: use Cauchy and safe-Dirichlet proposals.
    • Tunable proposals: new parameters for tuning the size of jumps.
    • Smarter tree/alignment SPR proposals.
  • Alignment Uncertainty (Au) Plots
    • Color by certainty (Rainbow) or by certainty+type (AA+fade).
    • Prettier/cleaner HTML output.
  • Easier to compile/install
    • Use autoconf for compilation.
    • Don't require external BOOST library.
    • Expanded description in User's Guide.
  • Easier to use
    • Windows version much improved.
    • Read configuration file ~/.bali-phy
    • Give helpful messages when errors occur.
    • Expanded User's Guide.
    • [workstations] Don't die when the user logs out.
    • [workstations] Don't die after 20 minutes when (soft) CPU limit expires.

comments and suggestions: benjamin . redelings * gmail + com