BAli---Phy

Release Notes

Version 3 (stable):
  • [3.0] - Feb-12-2018
  • [3.1] - Apr-??-2018
  • Speed & Memory
    • Speed: 0-300% faster.    Memory: 0-300% less memory.
    • [3.0] Better mixing when alignment depends on tree.
    • [3.0-beta4] Site-compression for fixed-alignment partitions.
  • Alignments
    • Allow analyzing 1-sequence and 2-sequence alignments.
    • [3.0-beta4] 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
    • New model language that allows setting all parameter values and priors:
      • --smodel=HKY[kappa=2]
      • --imodel=RS07[logLambda~Laplace[-4,0.707]]
    • Allow specifying priors on (i) shared branch lengths and (ii) partition-specific scale factors:
      • --branch-lengths=~iid[num_branches[T],Gamma[0.5,Div[2,num_branches[T]]]]
      • --scale=1,3:~Gamma[0.5,2]
    • Explicit priors, including default priors
    • [3.0] site-mixture models: Mixture[models=List[HKY,JC]]
    • [3.0] general site-rate distributions: HKY+MultiRate[Beta[2,3]]
    • [3.0] user-defined variables: let[m=HKY,Mixture[models=List[m,m,m+Rates.Gamma]]]
    • [3.0-beta5] priors for frequencies and GTR.
    • [3.0-beta5] super-long parameter names fixed.
    • [3.0-beta5] Codon and Triplet alphabets automatically determined from model.
    • [3.0-beta5] Triplet models + frequency models: (GTR+x3+MG94).
    • [3.0-beta6] sample initial branch-lengths from prior.
    • [3.0-beta5] alternative syntax linking partitions: --smodel 1:HKY --smodel 2:HKY --link 1,2
  • Summarization tools
    • [3.0-beta2] Beautify and condense MCMC statistics.
    • [3.0-beta4] Show 2-D MDS and 3-D topology convergence figures.
    • [3.0-beta2] Don't compute trace plots (too slow, large files).
  • Help
    • [3.0-beta4] Add diagnostics when loading codon sequences.
    • [3.0-beta5] Help for all command-line options via --help=<command>.
    • [3.0-beta5] Help for some models (e.g. --help=HKY) with citation info.
    • [3.0-beta5] Help levels via --help=simple|advanced|expert.
    • [3.0-beta5] --verbose flag gives readable information.
    • [3.0-beta6] Better help for functions.
    • [3.0-beta6] New syntax bali-phy help <topic>.
    • [3.1] Unix manual pages for bali-phy and tools
  • Misc
    • Add unit tests.
    • [3.0-beta2] Expand likelihood testsuite.
    • [3.0-beta6] Improve pre-burnin.
  • Install
    • [3.0-beta5] New install documentation.
    • [3.0-beta5] New homebrew tap for bali-phy.
    • [3.1] Debian package for bali-phy.
  • Compile
    • [3.0-beta5] Cairo library autodetected.
    • [3.0-beta6] Meson project files for building bali-phy.
    • [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).
    • [3.0-beta2] Rename parameter logs: *.p  →  *.log.
    • [3.0-beta2] Change spelling: gamma_inv  →  Rates.Gamma+INV.
    • [3.0-beta4] Change spelling: Gamma  →  Rates.Gamma.
    • [3.0-beta4] Change spelling: log-normal  →  Rates.logNormal.
    • [3.0-beta4] Change spelling: meanIndelLengthMinus1  →  meanIndelLength.
    • [3.0-beta5] Rename script: bp-analyze.pl  →  bp-analyze
    • [3.0-beta5] Shorter parameter names: INV.submodel.Rates.Gamma.submodel.F.pi.A  →  F:pi[A]
  • Fixes
    • [3.0-beta2] Fix compile on XCode 6.
    • [3.0-beta5] Fix crash on triplet models like TN+x3.
    • [3.0-beta6] Fix order of rate categories for DP model.
    • [3.0-beta6] Fix order of omega categories for M3 model.
    • [3.0-beta6] Fix very long initial tree.
    • [3.0-beta6] Make subsampling (-x number) work again for trees-consensus, etc.
    • [3.1] Fix crash in alignment-thin.
comments and suggestions: benjamin . redelings * gmail + com