Miscellaneous 2

  • PhyNav (Phylogenetic Navigator)
    A tree sampling method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method combines different methods to sample good trees. PhyNav homepage.

  • (p)IPHULA [(parallel) Inference of Population History Using a Likelihood Approach]
    (p)IPHULA is a software that investigates parameters of population history based on a Monte Carlo simulation using the maximum likelihood framework. IPHULA/pIPHULA homepage.

  • PluMiST - Plus and Minus SuperTrees
    PluMiST is a computer program to reconstruct and evaluate majority rule supertrees: MR(-), MR(+) and MR(+)g. The software is available at the PluMiST homepage.

  • SIMULATOR
    Software to simulate DNA and protein datasets with well-defined insertion-deletion dynamics according to a user-given tree. The software is available at the SIMULATOR homepage.

  • Shortest Triplet Clustering (STC)
    A new distance-based clustering method to reconstruct very large phylogenies in polynomial time O(n^2) for n sequences. The package is available at the STC homepage.

  • MRC.py
    is a computer program to evaluate the compatibility lengths given supertrees and gene trees and to extract the supertrees with the minimal lengths. The program is available at the MRC homepage.

  • GenerateTrees
    is a program to generate all or a random set of trees for a given set of taxon names. The package is available at the GenerateTrees homepage

  • Parat
    estimates site specific substitution rates from a set of DNA sequences. The package is available at the Parat homepage.


© 2016 CIBIV