Release Notes

See NEWS file for more details, and for older changes.

Version 3 (stable):
  • [3.0] - Feb-12-2018
  • [3.1] - May-02-2018
  • [3.2] - Jun-25-2018
  • [3.3] - Aug-06-2018
  • [3.4] - Dec-13-2018
  • Speed & Memory
    • Speed: 0-300% faster.    Memory: 0-300% less memory.
    • Site-compression for fixed-alignment partitions.
  • Alignments
    • Allow analyzing 1-sequence and 2-sequence alignments.
    • Include ancestral sequences in sampled alignments.
  • Large Trees
    • Compute likelihoods for very large trees (likelihood rescaling).
    • New treelength prior: don't prefer huge treelengths for trees with lots of leaves.
  • General
    • Add unit tests and likelihood testsuite.
    • [3.4] Allow selecting character sets from a file: sequences.fasta:100-240,300-900
    • [3.4] Allow recovering from initial -Infinity log-likelihood in MCMC.
    • [3.4] Install package manager bali-phy-pkg.
  • Models
    • Priors:
      • Explicit priors, including default priors
      • Sample initial branch-lengths from prior.
      • substitution model: -S 'hky85[kappa=2]'
      • insertion/deletion model: -I 'rs07[log_rate~laplace[-4,0.707]]'
      • branch lengths: -B '~iid[num_branches[T],gamma[0.5,div[2,num_branches[T]]]]'
      • partition-specific scale factors: -R '1,3:~gamma[0.5,2]'
    • New syntax:
      • let[m=hky85,mixture[models=List[m,m,m+Rates.gamma]]] (user-defined variables)
      • [3.3] function[w,gy94[omega=w]] (functions)
    • New models:
      • mixture[models=List[hky85,jc69]] (rates-across sites mixtures)
      • hky85+multi_rate[beta[2,3]] (rates-across sites with any distribution)
      • [3.3] +fe for equal frequencies.
      • [3.4] +mut_sel to add selection on a model.
    • RNA stem (16-state) models
      • [3.4] RNA models for fixed alignments. (Preliminary, because you have to pair the letters manually.)
      • [3.4] RNA stem models: RNA.16a, gtr_sym+x2_sym+f, gtr+x2+mut_sel
    • Codon and triplet models
      • [3.3] Improved codon models: gy94, mg94, f1x4, f3x4, gy94_ext, mg94_ext, x3, dNdS, etc.
      • [3.3] dNdS mixtures with mg94 and fMutSel: m3[function[w,fMutSel[omega=w]]]
      • [3.4] gtr+x3+dNdS+mut_sel (syntax for building up codon models piecewise)
  • Summarization tools
    • Show 2D & 3D topology convergencs figures (MDS).
    • [3.4] Reorganize logged statistics.
    • [3.4] Compute alignment summaries over all runs, not just the first one.
  • Help
    • Help for models, functions, distributions, and commands via bali-phy help topic.
    • [3.3] Rewrite documentation for substitution models and insertion/deletion models.
  • Tools
    • [3.4] cut-range: allow reading alignments from multiple files.
    • [3.4] alignment-distances: new tool, add accuracy and recal metrics
    • [3.4] tree-tool: scales trees, prunes trees, computes diameter, etc.
    • [3.4] alignment-thin: clean up options and man pages
    • [3.4] bali-subsample: rename from subsample to avoid conflict with phylobayes.
  • Install
  • Fixes
    • [3.3] Fix incorrect LG model.
    • [3.3] Fix run file for f81 model.
    • [3.3] bp-analyze: parse output files from 3.0-betal.
    • [3.4] Don't crash if the scale is set to a constant (e.g. --scale 1)
    • [3.4] Don't replace ambiguous nucleotides (W,N,etc.) in observed sequences unless given --set infer-ambiguous-observed=true
    • [3.4] Properly handle Newick labels with quotes or underscore.

comments and suggestions: benjamin . redelings * gmail + com