RT Journal
A1 Chen, Gary K.
A1 Marjoram, Paul
A1 Wall, Jeffrey D.
T1 Fast and flexible simulation of DNA sequence data
JF Genome Research 
JO Genome Research 
YR 2009 
FD January 01 
VO 19 
IS 1 
SP 136 
OP 142 
DO 10.1101/gr.083634.108 
UL http://genome.cshlp.org/content/19/1/136.abstract 
AB 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 (Markovian Coalescent Simulator), 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.