Software

ASMC (software, manual, paper, data). The Ascertained Sequentially Markovian Coalescent (ASMC) is a method to efficiently estimate pairwise coalescence times along the genome in SNP array or wholegenome sequencing data.

ARGON (software, paper) is a fast simulator of genetic data that samples from the discrete time WrightFisher process (DTWF) backwards in time. The coalescent is equivalent to the DTWF process if the sample size is small compared to the effective population size, but will deviate from it as the sample size increases. ARGON can simulate long chromosomes and large samples under the DTWF, with computational time comparable to recent coalescent simulators. It supports arbitrary demographic history, migration, variable mutation/recombination rates and gene conversion, and efficiently outputs pairwise identicalbydescent (IBD) sharing data.

IBDMUT (software, paper) estimates mutation and noncrossover gene conversion rates using identicalbydescent (IBD) segments shared by distant relatives within a population. The program implements two methods called tMRCA regression and MaAFthreshold regression. tMRCA regression estimates the mutation rate by regressing the number of observed sequence mismatches within IBD segments on the segments’ estimated age. The slope of this regression reflects the rate at which new mutations accumulate through time, while the intercept captures the genotyping error rate. This mutation rate estimate, however, may be biased due to noncrossover gene conversion events introducing high frequency standing variation in IBD regions. MaAFthreshold regression is used to simultaneously eliminte this bias and estimate the rate of noncrossover gene conversion events, exploiting the relationship between an allele’s frequency and the probability that it is involved in a gene conversion event.

DoRIS (software, paper1, paper2) is a tool for reconstructing finescale demographic events that occurred in the very recent past (e.g. ~100 generations) of one or multiple populations. Two randomly chosen individuals from the same population may share genetic relatives in the recent past. The average number of recent ancestors shared at a given point in time is inversely proportional to how large the population is: pairs of individuals from small population are more likely to be distant cousins than individuals from large populations. Similarly, two individuals from distinct groups that admixed very recently may share a number of common ancestors, depending on the rate at which their ancestors migrated across populations. Although we cannot directly observe the presence of past genetic ancestors, these hidden relationships often result in long genomic regions that are identicalbydescent (IBD) in groups of distant relatives, who are typically unaware of their relatedness. DoRIS infers the parameters of several possible demographic models using the density of IBD segments of different lengths. This type of analysis can reveal subtle population size fluctuations in the recent past (e.g. bottlenecks in the past 100 generations, see this paper), and relationships across groups within small geographic regions (e.g. within a country, see this paper).