4.0-beta17

This release speeds up likelihood calculations and adds some new codon models.

• Speed:
  • Use sparse likelihood vectors for leaf branches.
  • Use faster eigenvalue method to compute exp(Q*t) by default, falling back to slower method if needed.
• Models:
  • Multi-Nucleotide-Mutation (MNM) model for codons.
  • BUSTED and BUSTED-S substitution models for positive selection.
  • Initial cmdline version of multi_freq model.
• Bug fixes:
  • Sort the logged dN/dS values for m3_test
• Haskell:
  • Implement strict fields for data types with !type.
  • Improved error messages for type errors.

Release 4.0-beta16

• Speed: further speed up tree operations.
• Output: simplify results from ancestral sequence reconstruction.
• Input: allow defining models using multiple lines in control files.
• Models:
  • Speed up and improve RNA editing model.
  • Allow '--tree=~uniform_tree(taxa,gamma(0.5,2/length(taxa)))'
  • Allow Yule, coalescent, and uniform_rooted tree distributions.
• MCMC:
  • preliminary inference of rooted trees with alignments (NNI only, no SPR)
  • Use multiple transition kernels for uniform_int distribution.
  • Allow hand-written Metropolis-Hastings proposals for numbers/atomic objects.
• Bug fixes:
  • Fix crashes crashes on startup (in module writing/reading).
• Tests:
  • Refactor tests so that ninja test runs each testsuite test separately.
  • Add CI for ninja test.
• Haskell:
  • Fix [1.5 .. ] and ['a' ..] work for floating point.

Release 4.0-beta15

• Speed: reduce overhead in tree operations.
• Models: add relaxed-rs07 that allows rate to vary on different branches.
• Non-equilibrium models now work with variable alignments.
• Syntax: cmd-line functions now look like |w: gy94(omega=w)|
• Syntax: cmd-line functions can now take two arguments like |x y: x + y|.
• Bug fixes:
  • Fix inferring the alignment on a fixed topology (rooted or unrooted).
  • Invalidate compiled modules if the executable changes.
  • Fix consensus-tree and branch lengths ignoring burnin when not specified as percent.
  • Fix (unused) code that integrates out alignments when SPR-attaching on every branch.

Release 4.0-beta14

• Features
  • Allow inferring the number of bins under the Rates.free and M3 models.
  • Make startup faster by saving compiled modules.
  • Attempt to codesign executables on Mac.
  • Sort rates under Rates.free to make them identifiable.
  • Sort omegas under M3 to make them identifiable.
  • Allow specifying a discrete distribution on the command line like {value: prob, value: prob, etc.}
  • New distribution dirichlet_mixture to make variable-dimension mixtures easier.
• Bug fixes:
  • Infer the character state for N in leaf sequences with a fixed alignment.
  • bp-analyze should not fail when variables have random dimension.

Release 4.0-beta13

This release fixes a number of small bugs:

• Fix typo in bp-analyze script
• Fix crash in statreport
• Fix crash in draw-tree
• Fix crash in trees-bootstrap
• Add continuous-integration tests for post-processing.

Release 4.0-beta11

• Features

  • Improve alignment-thin --remove-gappy

• Bug fixes:

  • Fix warning in bp-analyze.
  • Only write warning in Rates.gamma at -V2 or higher.
  • Correctly compile with libfmt v10.
  • Complain instead of crashing when we use an imodel with --fix=alignment.

• Misc

  • JSON: read/write {Infinity, NaN} instead of {1e99999, null}
  • Make +> work like the R pipe operator.

Release 4.0-beta10

New features:

• Codon models can now use all known genetic codes (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
• Equilibrium non-reversible models now work with variable-alignment analyses.
• Improve help: colorized, improved signatures, more readable types.
• Add commands bali-phy print <expression>, bali-phy run <Prog> <arg1> <arg2>, bali-phy model <Model> <arg1> <arg2>.

Bug fixes:

• Fix non-standard genetic codes.
• Fix specifying Codons(DNA) and Codons(DNA, <code> )
• Fix density for Exp-transformed distributions like log-normal.

Misc:

• Refactor Numeric classes Log Double and Prob
• Allow testing isInfinite x and isNan x in Haskell.

Release 4.0-beta9

New features:

• allow "var1 ~ dist1; var2 ~ dist2; model(var1, var2)" in the command-line language
• non-reversible substitution models for fixed alignments (and for variable-alignments in the next pre-release)
• add Mac/ARM builds.

Fixes:

• fix quotes and _ in Nexus names
• fix numeric alphabets (e.g 0/1 characters)
• fix crash with long sequences
• fix crash in meson test

Release 4.0-beta8

This release has a number of changes under the hood, but not very many user-visible changes.

• Changes:
  • Write out tree with branch-lengths scaled according to weighted average of partition scales.
  • Print the alignment length including fixed-alignment partitions.
• Phylogenetics
  • Update likelihoods and other infrastructure to handle multifurcating trees and data on internal nodes.
• Tools
  • Add benchmarking script benchmark.py

Release 4.0-beta7

This release has a number of changes under the hood and a few visible changes to fix bugs:

• Allow estimating the alignment and branch lengths on a fixed topology: --tree=file.tre --fix topology
• Fix TSV logging when running generic models: -l tsv -m Model.hs