hmmIBD: software to infer pairwise identity by descent between haploid genotypes

Summary We introduce hmmIBD, software to estimate pairwise identity by decent between haploid genomes, such as those of the malaria parasite, sampled from one or more populations. We verified hmmIBD using simulated data, benchmarked it against a previously published method for detecting IBD within populations, and demonstrated its utility using Plasmodium falciparum data from Cambodia and Ghana. Supplementary information Supplementary data include Appendices S1, S2 and S3, and are available online. Availability and Implemetation Source code written in C99/C11-compliant C and requiring no external libraries, is freely available for download at https://github.com/glipsnort/hmmIBD/releases , alongside test datasets. Contact [email protected]