BIOINFORMATICS TOOLS

Informatics

ANCESTRY HUB

An ancestry server providing a local ancestry inference service for academics on high-throughput genome data (genotypes or haplotypes) using the aMAP pipeline

AMAP

 An novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry

Ma Y, Zhao J, Wong JS, Ma L, Li W, Fu G, Xu W, Zhang K, Kittles RA, Li Y, Song Q. Accurate inference of local phased ancestry of modern admixed populations. Scientific Reports. 2014 Jul 23;4:5800. PMID:25052506

AncestryView

This software draws ancestral analysis data into an image file with specified format and size using the Java graphical interface.

LASER

Determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types.

Li W, Fu G, Rao W, Xu W, Ma L, Shiwen Guo and Qing Song. GenomeLaser: fast and accurate haplotyping from pedigree genotypes. Bioinformatics. 2015 Dec 15; 31(24): 3984–3987. PMCID:  PMC5013932

HIFI

Using limited experimental seed data, HiFi can yield two integral, high-resolution personal chromosomal haplotypes in a cost- and time-efficient manner.
 
Rao W, Ma Y, Ma L, Zhao J, Li Q, Gu W, Zhang K, Vincent C Bond, and Qing Song. High-resolution whole-genome haplotyping using limited seed data. Nat Methods. 2013 Jan; 10(1): 10.1038/nmeth.2308. PMCID: PMC3835542 

Y5

It enables allele phasing from genotypes using limited sequence reads as initial input.

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Atlanta, Georgia, USA, 30033

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