Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species.

ABSTRACT: Admixture between populations provides opportunity to study biological adaptation and phenotypic variation. Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. Existing software packages for local ancestry inference are tuned to provide accurate results on human data and recent admixture events. Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species. Using simulations, we compare the performance of Loter to HAPMIX, LAMP-LD, and RFMix. HAPMIX is the only software severely impacted by imperfect haplotype re

SUBMITTER: Dias-Alves T 

PROVIDER: S-EPMC6107063 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature