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

ABSTRACT:

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 Gil

SUBMITTER: Sipos B 

PROVIDER: S-EPMC3102636 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature