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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 

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Context Dependent Mutation Rates

CIPI - Detecting context dependent mutation rates from NGS data

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FITS: Inferring POP-GEN parameters from time-series 

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

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

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

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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.

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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.

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