Fast and flexible simulation of DNA sequence data | Zendy

Gary K. Chen | Zendy; Paul Marjoram | Zendy; Jeffrey D. Wall | Zendy

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Fast and flexible simulation of DNA sequence data

Author(s) -

Gary K. Chen,

Paul Marjoram,

Jeffrey D. Wall

Publication year - 2008

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.083634.108

Subject(s) - coalescent theory , biology , linkage disequilibrium , haplotype , population , computer science , computational biology , genetics , theoretical computer science , algorithm , genotype , gene , phylogenetic tree , demography , sociology

Simulation of genomic sequences under the coalescent with recombination has conventionally been impractical for regions beyond tens of megabases. This work presents an algorithm, implemented as the program MaCS ( Ma rkovian C oalescent S imulator), that can efficiently simulate haplotypes under any arbitrary model of population history. We present several metrics comparing the performance of MaCS with other available simulation programs. Practical usage of MaCS is demonstrated through a comparison of measures of linkage disequilibrium between generated program output and real genotype data from populations considered to be structured.

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