MIXMUL – Estimating Haplotype Frequencies and Reconstructing Haplotypes from Mixed Genotype Data

MIXMUL

:: DESCRIPTION

MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

 MIXMUL

:: MORE INFORMATION

Citation

J Biomed Sci. 2009 Jun 2;16:52. doi: 10.1186/1423-0127-16-52.
A novel tool for individual haplotype inference using mixed data.
Lin CP, Fann CS.

PoolHap2 / PoolHapX 1.0.0 – Inferring Haplotype frequencies from Pooled Sequencing

PoolHap2 / PoolHapX 1.0.0

:: DESCRIPTION

PoolHap2 is a computer program that infers haplotype (or epitype in case of DNA methylation sequencing) from a pool.  In its current release, only pathogen sequencing application is implemented. In pathogen studies utilizing next generation sequencing, investigators ofte n collect samples naturally as pools of multiple strains, e.g., when the samples are taken from patients’ blood. To analyze these types of within-host polymorphisms, one would ideally like to determine the haplotypes in the sample. Even though isolation of single strains is possible by time-consuming experiments, the haplotype frequencies of different pathogen strains within a host are usually unknown, and this may well alter the initial within-sample frequencies. Here we developed Poolhap, a tool enabling researchers to infer the strain numbers and haplotype frequencies in silico from sequences of pooled samples.

The PoolHapX program reconstructs haplotypes within-host from pooled-sequencing data by integrating population genetic models (statistical linkage disequilibrium) with genomics reads (physical linkage). It approximate the resolution of single-cell sequencing using only pooled sequencing data, enabling within-host evolution analyses.

::DEVELOPER

Quan Long

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java

:: DOWNLOAD

 PoolHap , PoolHapX

:: MORE INFORMATION

Citation

Cao C, He J, Mak L, Perera D, Kwok D, Wang J, Li M, Mourier T, Gavriliuc S, Greenberg M, Morrissy AS, Sycuro LK, Yang G, Jeffares DC, Long Q.
Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.
Mol Biol Evol. 2021 May 19;38(6):2660-2672. doi: 10.1093/molbev/msab037. PMID: 33547786; PMCID: PMC8136496.

PLoS One. 2011 Jan 5;6(1):e15292. doi: 10.1371/journal.pone.0015292.
PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.
Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V, Ning Z, Tyler-Smith C, Nordborg M.

PoooL 1.1 – Estimate Haplotype Frequencies from large DNA Pools

PoooL 1.1

:: DESCRIPTION

PoooL is a novel constrained EM algorithm to estimate frequencies of single-nucleotide polymorphism (SNP) haplotypes from DNA pools. A quantity called importance factor is introduced to measure the contribution of a haplotype to the likelihood. Under the assumption of asymptotic normality of the estimated allele frequencies and a system of linear constraints on haplotype frequencies the importance factor remains a constant in the iterative maximization process.

::DEVELOPER

Han Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PoooL

:: MORE INFORMATION

Citation

Han Zhang, Hsin-Chou Yang and Yaning Yang
PoooL: An efficient algorithm for estimating haplotype frequencies from large DNA pools
Bioinformatics 2008 24(17):1942-1948