Table 1 Genome simulators

ART [9]

Simulation of sequence reads with error models for multiple platforms (454, Solexa, SOLiD).

Single or pair ended sequence reads.

MetaSIM [10]

Simulation of sequence reads for metagenomics, particularly for highly variable data (taxonomically distinct but related organisms).

Single or pair ended sequence reads.

GENOME [14]

Population simulation within a set of alleles using genome level events such as recombination, migration, bottlenecks, and expansions.

Alleles identified as mutated (1) or not (0) across the simulated population.

GWASimulator [12]

Simulation of loci across a population which follows a given LD structure in case–control type studies.

SNVs per individual for input loci.

FreGene [13]

Mutation simulation using a theoretical sequence of a given size with hotspot, conversion, and selection parameters.

Mutation selection across population for a theoretical sequence.

genomeSIMLA [11]

Simulation of disease loci within a family or case–control setting using specific LD patterns for investigations of disease.

Affy identified SNPs selected by disease association.

ALF [15]

Population simulation for a specific gene set using a model for variation at the sequence and individual level.

FASTA protein and DNA sequences for specific genes.