Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means of molecular data (e.g., DNA, RNA, amino acid or codon sequences). These relationships are typically described by means of a weighted tree, called a phylogeny, whose leaves represent the observed organisms, internal vertices the intermediate ancestors, edges the estimated evolutionary relationships, and edge weights a measure of the dissimilarity between pairs of organisms.

PhyloCoco
PhyloCoco is a simple tool for molecular phylogenetics able to rebuild phylogenies from DNA sequences under the likelihood or the minimum evolution criterion.

PhyloCoco key-features

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.] Specifically, PhyloCoco key-features are:

-The GTR model of DNA evolution.

-General additive distances [X. Gu and W.H. Li, A general additive distance with time-reversibility and rate variation among nucleotide sites, PNAS 93 (1996), 4671–4676].

-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 topological optimization.

-Iterated Local Search (ILS) to explore the solution space.

-Ant Colony Optimization (ACO) to explore the solution space under the minimum evolution criterion [D. Catanzaro, R. Pesenti and M. C. Milinkovitch, An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle,appeared in BMC Evolutionary Biology].

-FigTree to display the resulting phylogeny.

Requirements

A G4 or an intel core duo processor; Mac OS 10.4 or higher; Java 1.4 or higher.

Recommended

An intel core 2 duo; Mac OS 10.5.3 or higher; Java 1.5 or higher.

Contact
Daniele Catanzaro,
Service Graphes et Optimisation Mathématique (G.O.M.)
Computer Science Department

Université Libre de Bruxelles (U.L.B.)