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 [Superceded by CoalEvol].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 [Superceded by CoalEvol].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.
- NetTest: Mathematical characterization of phylogenetic networks.