Release Notes

See NEWS file for detailed change log.

Version 3 (stable):
  • [3.0] - Feb-12-2018
  • [3.1] - May-02-2018
  • [3.2] - Jun-25-2018
  • [3.3] - Aug-06-2018
  • 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.
  • 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.
    • Codon and triplet models
      • Codon and Triplet alphabets automatically determined from model.
      • [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]]]
      • [3.3] gtr+x3+dNdS (syntax for building up codon models piecewise)
    • Alternative syntax for linking partitions: --smodel 1:hky85 --smodel 2:hky85 --link 1,2
  • Summarization tools
    • Beautify and condense MCMC statistics.
    • Show 2D & 3D topology convergencs figures (MDS).
    • [3.1] Show priors.
    • [3.2] Reorganize HTML report.
  • Help
    • Add diagnostics when loading codon sequences.
    • Help for models/functions/distributions/commands via bali-phy help topic.
    • Give readable information under the --verbose flag.
    • [3.1] Unix manual pages for bali-phy and tools
    • [3.3] Rewrite documentation for substitution models and insertion/deletion models.
  • Misc
    • Add unit tests.
    • Expand likelihood testsuite.
    • Improve pre-burnin.
  • Install
    • New install documentation.
    • New homebrew tap for bali-phy.
    • [3.1] Debian package for bali-phy.
  • Compile
    • Autodetect Cairo library.
    • [3.1] Use Meson Build to build bali-phy, instead of autotools.
    • [3.1] Automatically use system libraries for boost, eigen, and nlohmann::json if available.
  • Changes
    • Simplify command-line options (some old options have been removed).
    • Rename parameter logs: C1.p  →  C1.log.
    • Rename script: bp-analyze.pl  →  bp-analyze
    • [3.1] Change spelling of many models/functions/distributions to lower-case.
  • Fixes
    • [3.1] Fix crash in alignment-thin.
    • [3.2] Fix prior on alpha in Rates.gamma.
    • [3.2] Link all programs with correct libstdc++ (Linux).
    • [3.2] Correctly record alignments for fixed-alignment partitions.
    • [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.

comments and suggestions: benjamin . redelings * gmail + com