PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

Background: The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity. Results: PhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Botond Sipos, Tim Massingham, Gregory E. Jordan, Nick Goldman
• Keywords: Artificial Intelligence, BMCBI 2011, Monte Carlo Simulation, Phylogenetic Inference Methods, Sequence Evolution