SABER specifications

Information


Unique identifier OMICS_02081
Name SABER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Hua Tang <>

Publication for SABER

SABER in publications

 (12)
PMCID: 4991838
PMID: 27436340
DOI: 10.1093/dnares/dsw029

[…] joint analysis of modern and ancient samples at a population level. tools and approaches (such as pca, structure, admixture, spamix, spa, admixtools, gps, lamp, hapmix, readmix, mutlimix, mspectrum, saber, and others) which were initially developed for population analysis of contemporary individuals, can be applied in combination with anthropological data and historical records to reconstruct […]

PMCID: 4749250
PMID: 26863142
DOI: 10.1371/journal.pgen.1005847

[…] colleagues analyzed a small cohort of puerto rican samples and reported three regions that are under strong recent selection []. using their then state-of-the-art local ancestry inference software saber [], tang and colleagues discovered in puerto rican samples genomic regions whose mean local ancestries (averaged over individuals) significantly deviated from the genome-wide average—a hallmark […]

PMCID: 4417236
PMID: 25902833
DOI: 10.1186/s12863-015-0196-x

[…] rely on reference allele frequencies for each parental population (i.e. lamp [] and those methods that utilize reference haplotypes for each of the ancestral populations (i.e. hapmix [], lamp-ld [], saber []) []. shriner et al. [] suggest that lamp-ld is among the most accurate software for local ancestry inference., in the current study, local ancestry was inferred using lamp-ld []. […]

PMCID: 5079159
PMID: 25043967
DOI: 10.1002/gepi.21835

[…] [], admixmap [], admixprogram [], and maldsoft []) use ancestry informative markers to track the ancestry variation across genome. lamp [] and winpop [] incorporated unlinked gwas chip genotypes. saber [] accounted for ancestral ld and allowed denser snps. hapmix [] and hapaa [] employed phased haplotypes, which largely improved the accuracy at the price of considerable computational […]

PMCID: 4080679
PMID: 25071832
DOI: 10.3389/fgene.2014.00204

[…] leverage the information that is available in haplotypes which can potentially be useful for distinguishing closely related populations. in contrast other methods that can explicitly model ld [e.g., saber: ; hapaa (hmm-based analysis of polymorphisms in admixed ancestries): ; hapmix: ] are computationally intensive and are able to consider only two ancestral populations at a time. lamp (local […]


To access a full list of publications, you will need to upgrade to our premium service.

SABER institution(s)
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

SABER reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SABER