Features

Features#

Phylogenetic models#

Tree model:

  • unrooted tree with branches lengths representing expected number of substitutions.

  • Time (rooted) tree with branch lengths representing units of time.

Substitution model:

  • Nucleotide models: JC69, HKY, GTR, SRD06. Any model nested within the GTR model using GeneralSymmetricSubstitutionModel.

  • Amino acid models: LG and WAG.

  • Codon model: Muse and Gaut (MG94).

  • Any discrete trait model (e.g. phylogeography model).

Rate heterogeneity across site: Constant, proportion of invariant sites, discretized Weibull distribution.

Molecular clock: strict and variable (i.e. one rate per branch).

Phylogenetic priors#

Unrooted tree branch lengths:

  • Exponential distribution (any appropriate distribution).

  • Compound gamma-Dirichlet prior.

Time tree:

  • Coalescent:

    • Constant and exponential growth population size.

    • Piecewise functions: skyride, skygrid (piecewise-constant on a grid), and skyglide (piecewise-linear on a grid).

  • Birth-death: constant, exponential, and BDSKY.

Molecular clock:

  • Strict: CTMC reference prior.

  • Variable: uncorrelated and correlated.

Inference algorithms#

Variational Inference:

  • Automatic Differentiation Variational Inference (ADVI).

Markov chain Monte Carlo (MCMC):

  • Vanilla MCMC.

  • Hamiltonian Monte Carlo (HMC).

Optimization:

  • Maximum a posteriori (MAP).

  • Maximum likelihood.