ArticleJournal of computational biology : a journal of computational molecular cell biology2011
Inference from samples of DNA sequences using a two-locus model.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
- KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation.Bioinformatics (Oxford, England) · 2021Article
- The distribution of waiting distances in ancestral recombination graphs.Theoretical population biology · 2021Article
- Partitioning, duality, and linkage disequilibria in the Moran model with recombination.Journal of mathematical biology · 2016Article
- Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.Genetics · 2016Article
- Stopping-time resampling and population genetic inference under coalescent models.Statistical applications in genetics and molecular biology · 2012Article
- TRACTABLE DIFFUSION AND COALESCENT PROCESSES FOR WEAKLY CORRELATED LOCI.Electronic journal of probabilityArticle
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Authors and funding
2 authors.
Funding
Abstract
Performing inference on contemporary samples of DNA sequence data is an important and challenging task. Computationally intensive methods such as importance sampling (IS) are attractive because they make full use of the available data, but in the presence of recombination the large state space of genealogies can be prohibitive. In this article, we make progress by developing an efficient IS proposal distribution for a two-locus model of sequence data. We show that the proposal developed here leads to much greater efficiency, outperforming existing IS methods that could be adapted to this model. Among several possible applications, the algorithm can be used to find maximum likelihood estimates for mutation and crossover rates, and to perform ancestral inference. We illustrate the method on previously reported sequence data covering two loci either side of the well-studied TAP2 recombination hotspot. The two loci are themselves largely non-recombining, so we obtain a gene tree at each locus and are able to infer in detail the effect of the hotspot on their joint ancestry. We summarize this joint ancestry by introducing the gene graph, a summary of the well-known ancestral recombination graph.
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