Release Notes

Older News

  • 10/25/05: version 1.9.8 released.
    • Documentation improvements.
    • Analysis phase: usability improvements.
    • Analysis phase: better handle partial partitions. (n-taxon statements)
    • FIX mistranslation of 3 codons.
    • FIX compilation on Mac OS X.
    • FIX crash with wildcards.
    • Print N or X for wildcard instead of *.
    • Allow user to specify alphabet more specifically.
    • Add alphabets for including STOP codon and amino acid.
  • 07/19/05: version 1.9.7 released.
    • Some speed/memory improvements.
    • FIX prior on mu.
    • FIX branch length proposals to include effect on alignment prior.
    • FIX Codon models - correctly find nucleotides inside codons.
    • FIX Codon models - scale branch lengths to match singlet models.
    • FIX Codon model YangM2
    • NEW indel model "fragments" that is time-independant
    • NEW asymmetric NNI and SPR proposals.
    • NEW documentation in HTML from docbook.
    • NEW statistics for transition kernels.
    • NEW tool: alignment-consensus.
    • NEW parameters for transition kernels.
  • 04/14/05: version 1.9.6 released.
    • SPEED improvements!
    • FIX Alignment constraints should work.
    • FIX Codon models to work again. YangM2 Codon model fixed.
    • NEW drawing schemes in alignment-draw...
    • NEW command line help availabe with "--help".
    • The form of arguments has changed to "--option arg" from "option=arg"
    • Setting/fixing/unfixing parameters works better now
    • Alignment format defaults to FASTA now
    • FASTA files should not contain blank lines between sequences!
  • 01/24/05: version 1.9.4 (BETA) released.
    • this release "should work" (many bugs fixed!).
    • use new indel model by default.
    • update tools to compile and work in new framework.
    • use less memory for conditional likelihoods.
    • initial support for multifurcating trees.
    • add invariant fraction to indel model.
    • add more color schemes to alignment-draw (needs more work).
    • speed up tree-dist-compare, print out M[l] consensus tree.
    • speed up alignment-gild: both I/O, and processing time.
    • speed up output (use buffered I/O).
    • speed up likelihood calculation, slightly.
    • speed up conditional likelihood calculations for DP.
    • fix fixing of parameters on command line.
    • put compiled tools in build/bin directory.
  • 12/23/04: version 1.9.3 (BETA) released.
    • fixed many bugs - but several remain.
    • removed internal copy of uBLAS matrix library. (use BOOST version).
    • started to update tools to match new tree code (not done).
    • started re-writing alignment-draw for more color-schemes (not done).
    • started dealing with std::bad_alloc() exception.
  • 11/27/04: version 1.9.2 (BETA) released.
    • improved indel model
    • alignment constraints
    • likelihood-caching to speed up likelihood calculation.
  • 09/16/04: version 1.8.24 released.
  • 06/28/04: version 1.8.14 developed (release notes)
    • Began version control (SubVersion)
    • No longer need uBlas "bindings"
  • 6/9/04: version 1.8.10 developed (release notes)

comments and suggestions: benjamin . redelings * gmail + com