MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent
Stephan Schiffels, Ke Wang
Abstract
The Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe the main program MSMC and its successor MSMC2. We go through all the necessary steps of processing genomic data from BAM files all the way to generating plots of inferred population size and separation histories. Some background on the methodology itself is provided, as well as bash scripts and python source code to run the necessary programs. The reader is also referred to community resources such as a mailing list and github repositories for further advice.
Topics & Concepts
Coalescent theoryScripting languageComputer sciencePython (programming language)PopulationEnsemblSuccessor cardinalSource codeMarkov processSoftwareProgramming languageBiologyGenomeGenomicsMathematicsGeneticsStatisticsSociologyGenePhylogenetic treeDemographyMathematical analysisGenetic diversity and population structureGenomics and Phylogenetic StudiesGenetic Mapping and Diversity in Plants and Animals