PHYML Unofficial versions

PHYMLrates

  • Author : Rachel Bevan (rachel@mcb.macgill.ca, McGill Centre for Bioinformatics, Montreal, Quebec, Canada).
    http://www.mcb.mcgill.ca/~rachel/

  • This version of PHYML implements the algorithm described in "Calculating the Evolutionary Rates of Different Genes: A Fast, Accurate Estimator with Applications to Maximum Likelihood Phylogenetic Analysis".
    Systematic Biology. 2005 54(6):900-915.

  • Download C source code (tar.gz archive).

    • PHYML - MPI

  • Author : Martha Torres (mxtd@uesc.br, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil).

  • This is a parallel version of PHYML. It only works when the bootstrap option is on.

  • Download C source code (tar.gz archive).

    • nhPHYML

  • Author : Bastien Boussau (boussau@biomserv.univ-lyon1.fr, Université Claude Bernard, Lyon, France). http://pbil.univ-lyon1.fr/software/nhphyml/

  • This is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of Galtier and Gouy (1998). As such, it provides estimates of the G+C contents of ancient sequences. It uses the algorithmic structure of PHYML adapted to the rooted and irreversible case. This algorithm has been described in an article "Efficient Likelihood Computations with Non-Reversible Models of Evolution", accepted for publication in Systematic Biology.

  • Download C source code (tar.gz archive).
    • If you want us to add a link to your (modified) version of PHYML, please feel free to send me (Vincent.Lefort@lirmm.fr) an e-mail with the sources and a few lines that describe in which aspects your version differs from the official one.