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.