PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
2011
PhyloSim: A Tool for Simulating Sequence Evolution
publication
Evidence: high
Author Information
Author(s): Sipos Botond, Massingham Tim, Jordan Gregory E, Goldman Nick
Primary Institution: EMBL-European Bioinformatics Institute
Hypothesis
Can we create a more realistic simulation framework for sequence evolution that overcomes the limitations of existing software?
Conclusion
PhyloSim offers unmatched flexibility for simulating sequence evolution under a wide range of realistic settings.
Supporting Evidence
- PhyloSim can simulate complex patterns of rate variation and multiple indel processes.
- It allows for user-defined complex patterns of mutation and selection.
- The framework is extensible and can be adapted to specific simulation needs.
Takeaway
PhyloSim is a computer program that helps scientists simulate how sequences of DNA change over time, making it easier to study evolution.
Methodology
PhyloSim uses the Gillespie algorithm to simulate substitutions, insertions, and deletions in sequences.
Limitations
The implementation in R may affect computing time and memory usage.
Digital Object Identifier (DOI)
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