PhyloCoco Icon

PhyloCoco

Minimalist tool for molecular phylogenetics.

PhyloCocoOverview

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.

NEW

Fixed some bugs.

PhyloCocoInformation

Version
2.3
Date
03.18.10
License
Free
Language
English
File Size
3.9MB
SubCategory
Operating Systems
Mac OS X
System Requirements
No additional system requirements.
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