An R package for the Monte Carlo simulation of sequence evolution Long Description (required) 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 of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs. Key features of PhyloSim include
1) Simulation of the evolution of a set of discrete characters with arbitrary states evolving by a continuous-time Markov process with an arbitrary rate matrix.
2) Explicit implementations of the most popular substitution models (nucleotide, amino acid and codon substitution models).
3) Simulation under the popular models of among-sites rate variation, like the gamma (+G) and invariant sites plus gamma (+I+G) models.
4) The possibility to simulate under arbitrarily complex patterns of among-sites rate variation by setting the site specific rates according to any R expression.
5) ... please refer to our documentation for details. http://www.ebi.ac.uk/goldman-srv/phylosim/ None Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator. Every sub-attribute is selected Not all sub-attributes are selected Fill Clear Expand Collapse Reset Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s). Can't Find the Attribute You Are Looking For?
If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the
Additional Comment box of the Submit tab. Summary of Proposed Changes Current Citations/Applications
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. BMC Bioinformatics,
https://www.ncbi.nlm.nih.gov/pubmed/?term=21504561, Primary Citation