Computational Phylogenetics
... Molecular Data, Evolutionary Modeling and Computational Tools

KCM

KCM is a software to infer models of codon evolution using the generalization described in Zaheri et al (2014; MBE). The software is based on codeml from the PAML package and uses the same configuration file and input files as codeml.

Written on Wednesday September 24, 2014

PyRate

PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data. We developed a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We further implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models.

Written on Tuesday March 4, 2014

FastCodeML

FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution (Yang and Nielsen, 2002, Mol Biol Evol). Although the model is similar to the one implemented in the codeml software from the PAML package, our goal was to focus on the computational efficiency by developing an improved serial implementation but also provide new parallelisation strategies.

By using an hybrid (OpenMP/MPI) strategy, FastCodeML can reach a speed-up of up to 10 times compared with codeml. The speed-up will increase with larger data sets.

Written on Tuesday March 4, 2014

Jive

You can download the R source code for the Jive package here.

This package includes functions to analyse phenotypic data using a hierarchical Bayesian model that accounts for intraspecific variation. The publication is in preparation for Systematic Biology (Kostikova et al. in prep). An example of the application is in press in Proc R Soc B (Litsios et al. in press).

Written on Thursday February 20, 2014

Other software

You will find here several software that were developped for various tasks. The source code is provided in the tar ball that can be downloaded. Please note that no support is provided for them.

Written on Monday February 10, 2014

TreeCorrect

TreeCorrect is a software to compute percentages of tree correct or correct tree. A tree or a series of subtree that you want to compare to your tree file can be used as the "true" tree. It is written in Java and is available for Linux, Mac OS X and Windows operating systems.

Written on Tuesday October 22, 2013

MLTree

MLtree is a software that implements maximum likelihood estimation of model parameters given a fixed topology with user-defined branch lengths. It includes DNA model of substitution as well as a serie of Markov model designed for 2-states characters.

Written on Tuesday October 22, 2013

Script Serrano et al

You will find here the scripts for the papers of Martha Serrano:

  • Serrano et al (2015; BMC Evol Biol) are available here.
  • Serrano et al (submitted; Proc R Soc B) are available here.

Written on Sunday October 6, 2013

Coev

Coev is a software that predicts coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree.

Written on Friday January 31, 2014

SuperTree

SuperTree is a software to build phylogenetic supertrees. In its current version, it implements the MRP algorithm to assemble source trees into a supertree. It is written in Java and is available for Linux, Mac OS X and Windows operating systems.

Written on Sunday October 6, 2013