Simulation of Genetic Data

• ReCodon: Simulation of coding sequences with  recombination, migration and demographics. [Superceded by CoalEvol].
• NetRecodon: Simulation of coding sequences with intracodon recombination, migration and demographics. [Superceded by CoalEvol].
• CoalEvol: Simulation of DNA, codon and aminoacid sequences under different population models.
• SGWE: Simulation of genome-wide evolution with different substitution models among partitions.
• ProteinEvolver: Simulation of protein evolution accounting for structural constraints.
• SPLATCHE3: Simulation of genetic data (DNA, SNP, STR) under spatially-explicit evolutionary scenarios. In collaboration with Mathias Currat, Claudio Quilodran, Laurent Excoffier and Nicolas Ray (main developers).

Analysis of Genetic Data

• ProtASR: Ancestral sequence reconstruction of proteins accounting for structural constraints.
• CodABC: Coestimation of recombination, substitution and dN/dS in multiple alignments of coding sequences using approximate Bayesian computation.
• ProteinEvolverABC: Coestimation of recombination and substitution rates in multiple alignments of protein sequences using approximate Bayesian computation.
• ProteinModelerABC: Selection among substitution models of protein evolution that consider the protein structure using approximate Bayesian computation. The main developer is David Ferreiro.
• NetTest: Mathematical characterization of phylogenetic networks.