SABER is a program suitable for genome-scale data which uses a “Markov-hidden Markov model” to estimate local ancestry (Tang H, Coram M, Wang P, Zhu X, Risch NJ. (2006) Reconstructing Genetic Ancestry Blocks in Admixed Individuals. Am J Hum Genet. 79:1-12.). This local ancestry is referred to as “ancestral blocks”. Like HAPMIX, it models the ancestral LD; however it does not model haplotype structure. Input files are typical and include genotype data from ancestral and admixed individuals, global ancestry estimates of admixed individuals, and physical map location of the SNPs. In addition to providing localized ancestry (with graphical output), SABER can be used to estimate time since admixture. Reconstructing Genetic Ancestry Blocks in Admixed Individuals
Keywords for this software
References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- Buzbas, Erkan Ozge; Verdu, Paul: Inference on admixture fractions in a mechanistic model of recurrent admixture (2018)
- Chen, Hua; Hey, Jody; Slatkin, Montgomery: A hidden Markov model for investigating recent positive selection through haplotype structure (2015)
- Yushi Liu, Toru Nyunoya, Shuguang Leng, Steven A Belinsky, Yohannes Tesfaigzi, Shannon Bruse: Softwares and methods for estimating genetic ancestry in human populations (2013) not zbMATH
- Boca, Simina M.; Rosenberg, Noah A.: Mathematical properties of (F_\mathrmst) between admixed populations and their parental source populations (2011)