SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history | Zendy

Guillaume Laval | Zendy; Laurent Excoffier | Zendy

Open Access

SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history

Author(s) -

Guillaume Laval,

Laurent Excoffier

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth264

Subject(s) - coalescent theory , nucleotide diversity , software , computer science , extension (predicate logic) , diversity (politics) , set (abstract data type) , population , biology , computational biology , genetics , haplotype , programming language , allele , gene , demography , sociology , anthropology , phylogenetic tree

We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias.

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