is a minimalist tool for molecular phylogenetics able to rebuild phylogenies by means of the likelihood criterion. Phylococo automatically selects the best substitution model of DNA evolution for the dataset of sequences to be analyzed and display after a short time the best so far phylogeny found.
PhyloCoco implements the algorithms described in [D. Catanzaro, R. Pesenti and M. C. Milinkovitch. Estimating phylogenies under maximum likelihood: a very large-scale neighborhood approach. Submitted to BMC Bioinformatics. Currently under second revision] and hereafter summarized:
- The GTR model of DNA evolution.
- Random Directions, Brent's algorithm and Random Search for unconstrained non-linear optimization of the likelihood parameters.
- Very Large Scale Neighborhood (VLSN) search for the topology optimization.
- Iterated Local Search (ILS) to explore the solution space.
PhyloCoco uses figtree to display the resulting phylogeny.