M E TA P I G A V.

3 I S A V A I L A B L E F O R D O W N L O A D (with Codon models, GPU computing, and more)

MetaPIGA is a versatile and easy-to-use software that implements robust stochastic heuristics (including the Metapopulation Genetic Algorithm, metaGA) for large phylogeny inference under maximum likelihood. MetaPIGA allows analyses of binary and molecular data sets under multiple substitution models, Gamma rate heterogeneity, and data partitioning. The software is for all types of users as it can be run through an extensive and ergonomic graphical interface or by using batch les and console interface on your local machine or on distant servers. MetaPIGA is platform independent, runs on 32- and 64-bits systems, and easily takes advantage of multiprocessor and/or multicore computers. Here, we release the version 3 of MetaPIGA which, besides bug xes, includes new functionalities such as: Maximum likelihood models for codon evolution (Goldman-Yang 1994 and Empirical Models) with access to multiple genetic codes (universal, mitochondria, chloroplaste, etc); Likelihood computation on CUDA-compatible Nvidia graphic cards (reducing run time by a factor of 10 to 20 for Protein/Codon data); Ancestral-state reconstruction using empirical Bayesian inference. Some of the other functionalities implemented in MetaPIGA are: Simple data quality control (testing for the presence of identical sequences as well as of excessively ambiguous or excessively-divergent sequences); Automated trimming of poorly aligned regions using the trimAl algorithm; The Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion methods for easy selection of the substitution model that best ts your data; Detailed monitoring of run progress; Convergence statistics for automatically dening when an analysis is complete; Ancestral-state reconstruction of all nodes in the tree; Viewing and manipulation of result trees. MetaPIGA v.3 and its manual can be downloaded from the new website at www.metapiga.org. Dont hesitate to contact us (Dorde.Grbic@unige.ch or Michel.Milinkovitch@unige.ch) for additional questions, assistance, or bug reports. -------------------------------------------------------------------------------------Laboratory of Articial & Natural Evolution (LANE) www.lanevol.org Dept of Genetics & Evolution University of Geneva Science III, quai Ernest Ansermet 30 1211 Geneva, Switzerland --------------------------------------------------------------------------------------