- 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)
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