Phylograd: fast column-specific calculation of substitution model gradients.

ABSTRACT:

Background

Most popular tools for reconstructing phylogenetic trees from multiple sequence alignments use a model of molecular evolution in which a single substitution matrix or a small set of fixed matrices are shared between all columns. Models with column-specific rate matrices can in principle be fit by automatic differentiation methods, but in practice the heavy computational burden associated with computing the gradients of the many matrix exponentials has hindered exploration of such models.

Implementation

Here, we present a highly efficient approach for reverse-mode differentiation of the log likelihood computed with Felsenstein's algorithm under any time-reversible substitution model. PhyloGrad is implemented in Rust and has Python bindings to easily combine it with

SUBMITTER: Lieser B 

PROVIDER: S-EPMC12836810 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature