BAli---Phy

Release Notes

See NEWS file for detailed change log.

• 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.