ArticleMolecular biology and evolution2013
Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Article
- PolyAdapt: Characterizing Polygenic Adaptive Architectures in the Presence of Strong Linkage Disequilibrium.Genome biology and evolution · 2026Article
- The illusion of polygenicity in pool-seq genetic mapping studies: insufficient power can mask simple genetic architectures.Genetics · 2026Article
- Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.Molecular biology and evolution · 2026Article
- Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts.The ISME journal · 2026Article
- Variation in the resource environment affects patterns of seasonal adaptation at phenotypic and genomic levels inEvolution letters · 2025Article
- Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160).BMC bioinformatics · 2025Article
- Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection.Nature ecology & evolution · 2025Article
- Pervasive fitness trade-offs revealed by rapid adaptation to shifting population densities in large experimental populations ofbioRxiv : the preprint server for biology · 2025Article
- "Select and Resequence" Methods Enable a Genome-Wide Association Study of the Dimorphic Human Fungal Pathogen Coccidioides posadasii.Genome biology and evolution · 2025Article
- Virulence is not directly related to strain successmSystems · 2025Article
- Article
- grenedalf: population genetic statistics for the next generation of pool sequencing.Bioinformatics (Oxford, England) · 2024Article
- Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data.BMC bioinformatics · 2023Article
- Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate supply in Arabidopsis.PLoS genetics · 2023Article
- Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes.Molecular biology and evolution · 2022Article
- grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads.Bioinformatics (Oxford, England) · 2022Article
- Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability.Evolution; international journal of organic evolution · 2022Article
- Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype.Applied and environmental microbiology · 2022Article
- Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont.Proceedings. Biological sciences · 2022Article
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3 authors.
Funding
Abstract
DNA samples are often pooled, either by experimental design or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of sequencing. Alternatively, the sample itself may be a mixture of multiple species or strains (e.g., bacterial species comprising a microbiome or pathogen strains in a blood sample). We present an expectation-maximization algorithm for estimating haplotype frequencies in a pooled sample directly from mapped sequence reads, in the case where the possible haplotypes are known. This method is relevant to the analysis of pooled sequencing data from selection experiments, as well as the calculation of proportions of different species within a metagenomics sample. Our method outperforms existing methods based on single-site allele frequencies, as well as simple approaches using sequence read data. We have implemented the method in a freely available open-source software tool.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.