Phyldog is a program made to simultaneously build gene and species trees when gene families have undergone duplications and losses. It can analyze thousands of gene families in dozens of genomes simultaneously, and was presented in an article in Genome Research. Trees and parameters are estimated in the maximum likelihood framework, by maximizing the probability of alignments given the species tree, the gene trees and the parameters of duplication and loss.
It is built on the Bio++ and BOOST C++ libraries, and uses MPI for parallelization.
It is provided as is and should be used with appropriate care.
- Homepage: http://pbil.univ-lyon1.fr/software/phyldog/
- laboratory_name: LBBE / CNRS 5555
Project Manager: Thomas Bigot