RERconverge on GitHub
RERconverge is a set of software written in R that estimates the correlation between relative evolutionary rates of genes and the evolution of a convergent binary or continuous trait across a phylogeny.
Full step-by-step instructions (pdf or html) on how to identify genetic elements correlated with the convergent evolution of your trait of interest.
ERC Analysis Webserver
ERC measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. High ERC values are typically observed between genes participating in a common pathway or that otherwise share functionality.
Datasets and Repositories Accompanying Papers
2022 Lucas et al. “Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa”
Multiple sequence alignments and phylogenetic trees. aln_trees.zip sea-urchin-msa.fa
2019 Raza et al. PLOS Genetics [ https://datadryad.org/stash/dataset/doi:10.5061/dryad.fp45s43 ]
Data from: Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila
2018 Meyer et al. Science. [ https://github.com/nclark-lab/MarineFxLoss ]
This repository contains scripts associated with a genome-wide screen for convergent loss of gene function in marine mammals.
2012 Clark, Alani, Aquadro. Genome Research
ERC Yeast Dataset 2012
[zip file yeastERC ]