phyloConverge

phyloConverge is a comparative genomics software for identifying phenotypic associations of genetic elements.

phyloConverge combines maximum likelihood estimation and phylogeny-aware permutation tests to detect significant convergent evolutionary rate shifts underlying phenotypic convergence, while calibrating for biases from phylogenetic dependence, sequence genomes, and correlations between genetic elements. phyloConverge is able to analyze segments of nucleotides at a wide range of sizes, from scoring genes or conserved elements, to scanning entire multiple sequence alignments at nucleotide resolution with computational tractability.

Dependencies

phyloConverge requires the following to be installed:

• RERconverge

  • Follow installation here: RERconverge

• RPHAST

  • Follow installation here: RPHAST or here

Installation

phyloConverge can be installed using the devtools package, using the following command:

library(devtools)
install_github("ECSaputra/phyloConverge")

Example Use

For examples on how to run phyloConverge, please refer to this walkthrough.