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 [Superceded by CoalEvol].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 [Superceded by CoalEvol].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