Bayesian estimation of lineage specific substitution rates in conserved non-coding regions while accounting for phylogenetic discordance
For those with the most up to date version of Anaconda installed, you can install PhyloAcc with bioconda in a fresh environment with a single command:
conda install phyloacc
For more help or troubleshooting installation, please see the Install page.
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.
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