Sebastian E. Ramos-Onsins* and Thomas
Mitchell-Olds**

Previous address: Max-Planck Institute of Chemical Ecology

Present address: *Universitat de Barcelona; **Duke University

Previous address: Max-Planck Institute of Chemical Ecology

Present address: *Universitat de Barcelona; **Duke University

mlcoalsim : Multilocus Coalescent Simulations

Current Released Version: 1.42 (March 18th, 2008)

Current Released Version: 1.42 (March 18th, 2008)

The application program mlcoalsim is designed to:

- Generate samples and calculate neutrality tests, and other statistics, under several demographic models and also strong positive selection using the coalescent theory.
- Perform coalescent simulations given:
- the population mutation rate theta (4Nu, where N is the effective population size and u is the mutational rate).
- a fixed number of mutations.
- a fixed number of mutations but taking into account a distribution of the population mutation rate. A uniform, log-uniform and gamma distributions are included.
- Perform coalescent simulations considering recombination and using:
- the population recombination rate theta (4Nr, where N is the effective population size and r is the recombination rate).
- a fixed number of Rm and considering a distribution of the population recombination rate. A uniform, log-uniform and gamma distributions are included.
- a fixed number of Rm and number of haplotypes and considering a distribution of the population recombination rate.
- Perform multilocus analyses. Linked loci and unlinked loci are enabled. Multilocus statistics for unlinked loci are the average and the variance for each statistic.
- Include recurrent mutations (multiple hits).
- Include heterogeneity in the mutation and recombination rate across the sequence (using a gamma distribution).
- A number of invariant sites for mutation can be defined for each locus.
- Calculates the likelihood value for a number of observed values statistics.

Remember: mlcoalsim is optimized for many independent regions, or alternatively, for linked regions when the recombination value is not too large. In case using large recombination values (i.e., large genome regions), ancestral recombination graph (ARG) is a much faster methodology and should be used.

Download

- version 1.42

http://code.google.com/p/mlcoalsim-v1/downloads/list

- Documentation for
mlcoalsim version 1.42:

manual_mlcoalsim.pdf

- Related applications: three
perl
scripts to help in the analyses:

related applications (zip)

- mlcoalsim examples: input data
files and outputs:

examples version 1.42 (zip)

- Previous versions

GNU General Public License

This program is distributed under the GNU General Public License:

GNU_GPL_License.txt

Bug Reports

Please send your questions, comments and bug reports to Sebastian E. Ramos-Onsins at:

Reference

Sebastian E. Ramos-Onsins and Thomas Mithell-Olds. mlcoalsim: Multilocus Coalescent Simulations.

Evolutionary Bioinformatics 2007:2 41-44.

visitors since January, 2007.

March 18th, 2008