Bayesian estimation of lineage specific substitution rates in conserved non-coding regions while accounting for phylogenetic discordance

Install

For those with the most up to date version of conda and mamba installed, you can install PhyloAcc with bioconda in a fresh environment with a single command:

You can also use conda install phyloacc to install PhyloAcc instead of mamba, though mamba is recommended for faster installation.

For more help or troubleshooting installation, please see the Install page.

About

PhyloAcc is a program to detect shifts of DNA substitution rates in noncoding, conserved genomic regions. It can be used to identify genomic elements that have experienced accelerated rates along certain lineages in a phylogeny. This can be used, for example, to identify convergent rate shifts that coincide with phenotypic convergence.

Substitution rates are estimated per lineage in the input species tree while accounting for underlying phylogenetic discordance. Three separate models are fit to the data: one allowing only conserved or background rates on all lineages, one allowing accelerated rates on specified target lineages, and a full model that allows accelerated rates on every lineage. The likelihoods of these nested models are compared for each element with Bayes Factors and questions can be formulated based on these comparisons.

Citations

Yan H, Hu Z, Thomas GWC, Edwards SV, Sackton TB, Liu JS. 2023. PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts on targeted lineages accounting for gene tree discordance. Molecular Biology and Evolution 10.1093/molbev/msad195

Version 1 (the "species tree" version):

Hu Z, Sackton TB, Edwards SV, Liu JS. 2019. Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Molecular Biology and Evolution 10.1093/molbev/msz049