About PhyloCoco
A minimalistic tool for molecular phylogenetics able to recover phylogenies from nucleotide sequences. PhyloCoco uses the likelihood or the minimum evolution criterion, and automatically selects the best substitution model of DNA evolution for the dataset analyzed. PhyloCoco key-features are:

- The GTR model of DNA evolution.
- General additive distances for minimum evolution [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 (see http://www.biomedcentral.com/1471-2148/7/228/abstract).

What’s New in this Version
- improves the stability of the whole graphical application;
- fixes several bugs affecting the opening of nexus files;
- supports the least version of FigTree;
- includes an automatic check for updates.