Tools

The lab has been involved in the development of several tools encompassing the detection of positive selection and coevolution in molecular sequences to the modeling of phenotypic traits across the branches of a phylogenetic tree.

Here’s the list of the main software that we maintain

  • FastCodeML: estimation of positive selection on multiple sequence alignments
  • Coev: estimation of coevolution between pairs of sites along a sequence
  • Coev-web: web interface for the Coev model
  • CoevRJ: inferring coevolution and phylogenetic trees using MCMC
  • PyRate: estimation of rates of diversification from fossils data
  • scripts from Serrano-Serrano et al. 2015
  • JIVE: trait evolution accounting for intra-specific variance
  • FossilBM: estimating evolutionary rates and trends by integrating fossil and phylogenetic data