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MSMC

MSMC

Description

This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences.

In short, msmc can infer

  • the scaled population size of a single population as a function of time
  • the timing and nature of population separations between two populations

from multiple phased haplotypes. When only two haplotypes are given, MSMC is similar to PSMC, and we call it PSMC' because of subtle differences in the method and the underlying model, which allows PSMC' to infer more accurately the recombination rate.


Available

Version on CSC's Servers


Taito: msmc


Usage

To load MSMC:

module load python-env/3.4.1
module load msmc
Note that the MSMC module can also be loaded directly. Python is only needed if you wish to use the msmc-tools scripts (bamCaller.py etc)


Discipline

Biosciences

References

Inferring human population size and separation history from multiple genome sequences. Stephan Schiffels & Richard Durbin, Nature Genetics 46, 919–925 (2014) doi:10.1038/ng.3015


Support

servicedesk@csc.fi


Manual

Short guide to MSMC