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
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.
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.