Software & Data
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.
Detecting parallel selection in phylogenetic data: sites where two or more substitutions occurred in independent lineages of the phylogeny, and were driven by selection.
Detecting lateral gene transfer via swapping of two non-homologous enzymes
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.
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.