PhyloCoco PhyloCoco - A simple tool for molecular phylogenetic estimation.
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PhyloCoco Tags

molecule phylogenetic rebuild molecular phylogenetics rebuild phylogenies likelihood criterion

PhyloCoco Description

PhyloCoco - A simple tool for molecular phylogenetic estimation. PhyloCoco is a free and minimalist tool for molecular phylogenetics that is 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.Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means of molecular data. These relationships are typically described through a weighted tree, called phylogeny, whose leaves represent the observed organisms, internal vertices represent the intermediate ancestors, and the edges represent evolutionary relationships between pairs of organisms.Here are some key features of "PhyloCoco":· The GTR model of DNA evolution.· Gamma distribution to model among site rate heterogeneity.· 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 PaloAlto to display the resulting phylogeny.Requirements:· A G4 or an intel core duo processor· Java 1.4 or higher. Recommended:· An intel core 2 duo· Java 1.5 or higher. What's New in This Release: · improves speed and stability of the whole graphical application · supports FigTree 1.2.1

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