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.
