Title |
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees
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Published in |
BMC Bioinformatics, September 2015
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DOI | 10.1186/s12859-015-0721-y |
Pubmed ID | |
Authors |
Sha Zhu, James H. Degnan, Sharyn J. Goldstien, Bjarki Eldon |
Abstract |
There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution. |
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