Release Notes
Version 2.2:
- [2.2.0] - 12-30-2013
- [2.2.1] - 03-20-2014
- Internals
- New model representation framework
- Models
- site-dependent codon models: M1a, M2a, M2a_Test.
- branch and site-dependent codon models: branch-site.
- frequency models: +F, +gwF, F1x4, F3x4, MG94, MG94w9, F61.
- Output
- Inference of ancestral sequences at internal nodes (optional).
- Trees are written with names for internal nodes.
- Allow computing Rao-Blackwellized expectations for some variables.
- Input
- Substitution models may now take multiple arguments: branch-site[2,HKY,F3x4].
- Speed
- Lazily calculate eigensystems for substitution rate matrices.
- [0-100% slower] Rewrite model framework.
- Summarization tools
- alignment-cat: improved ability to select, reorder, strip gaps, and reverse the input sequences.
- trees-consensus: allow reading trees with node and branch attributes
- trees-consensus: allow reading trees with internal node names
- [2.2.1] Make post-processing accept line endings in Linux/Mac/Windows format.
- Build
- Stop depending on the GSL library.
- Switch to C++11.
- Changes
- 'lambda' renamed to logLambda.
- 'epsilon' replaced with meanIndelLengthMinusOne.