BAli---Phy

News

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.

---

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)