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