Software & Data

All of our newer projects have code on GitHub - check them out here

PhyVirus: a phylogenetic based dataset of ssRNA viral sequences

Dataset of coding sequences of single-strand RNA viruses

Context Dependent Mutation Rates

CIPI - Detecting context dependent mutation rates from NGS data

FITS: Inferring POP-GEN parameters from time-series

Inferring population genetics parameters (fitness, mutation rate, or population size) from temporal deep sequencing data.

ParaSel

Detecting parallel selection in phylogenetic data: sites where two or more substitutions occurred in independent lineages of the phylogeny, and were driven by selection.

LGT3State

Detecting lateral gene transfer via swapping of two non-homologous enzymes

RASER

A likelihood based method for testing and detecting site-specific evolutionary rate shifts. Given a multiple sequence alignment (MSA) and a phylogenetic tree, the program determines:
(a) Whether or not site-specific rate shifts characterize the evolution of a protein, and
(b) If so, points to the specific sites and lineages in which these shifts have most likely occurred.

Selecton

web-server for the detection of site-specific evolutionnary rates, measured as Ka/Ks, the ratio between the non-synonymous to synonymous rate at each site.