mlcoalsim

mlcoalsim Software

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

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.

This program is based on a previous version of Hudson’s coalescent program ms (Hudson, 2002) and modified for the above purposes.

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

- Complete download: mlcoalsim package, including source files, documentation, examples and executables:
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

        - Previous versions are not mantained anymore.

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