Abstract
BackgroundThe development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities.ResultsHere, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers.ConclusionsThe metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.
Highlights
The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences
That objective remained intractable in practice because of (a) the NP-hard nature of optimality-criterion-based phylogeny inference and (b) the computing-time requirements of using complex substitution models in the framework of what had been identified as the probable most robust optimality criterion: Maximum Likelihood (ML; [16,17,18])
One key advance that made large phylogeny inference tractable is the implementation in this field of stochastic heuristics with inter-step optimization, i.e., a family of approaches that existed for decades in physics and computer science and explore multidimensional solution spaces in a much more efficient manner than the older intra-step optimization hill-climbing methods
Summary
The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. One key advance that made large phylogeny inference tractable is the implementation in this field of stochastic heuristics with inter-step optimization, i.e., a family of approaches that existed for decades in physics and computer science and explore multidimensional solution spaces in a much more efficient manner than the older intra-step optimization hill-climbing methods. In the latter, one prime parameter (typically, the topology of the tree) is modified and all other parameters are optimized before the new solution is evaluated whereas, in stochastic heuristics, all free parameters are optimized while the search proceeds.
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