ArticleBioinformatics (Oxford, England)2021
KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 31 citations in OpenAlex.
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches.Frontiers in bioinformatics · 2026Review
- Moonshine.jl: a Julia package for genome-scale model-based ancestral recombination graph inference.Frontiers in genetics · 2026Article
- A general framework for branch length estimation in Ancestral Recombination Graphs.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A General Framework for Branch Length Estimation in Ancestral Recombination Graphs.bioRxiv : the preprint server for biology · 2025Article
- Allele age estimators designed for whole-genome datasets show only a moderate reduction in performance when applied to whole-exome datasets.G3 (Bethesda, Md.) · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- tskit_arg_visualizer: interactive plotting of ancestral recombination graphs.Bioinformatics advances · 2025Article
- Inference and applications of ancestral recombination graphs.Nature reviews. Genetics · 2025Review
- Constructing ancestral recombination graphs through reinforcement learning.Frontiers in genetics · 2025Article
- Article
- Evolution of Phytophthora infestans on its potato host since the Irish potato famine.Nature communications · 2024Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Accurate inference of population history in the presence of background selection.bioRxiv : the preprint server for biology · 2024Article
- Global and Local Ancestry and its Importance: A Review.Current genomics · 2024Review
- Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests.Systematic biology · 2023Article
- Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks.Molecular biology and evolution · 2023Article
- Demographically explicit scans for barriers to gene flow using gIMble.PLoS genetics · 2023Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Review
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
motivationThe reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG, which implements a parsimony-based greedy heuristic algorithm for finding plausible genealogical histories (ancestral recombination graphs) that are minimal or near-minimal in the number of posited recombination and mutation events.
resultsGiven an input dataset of aligned sequences, KwARG outputs a list of possible candidate solutions, each comprising a list of mutation and recombination events that could have generated the dataset; the relative proportion of recombinations and recurrent mutations in a solution can be controlled via specifying a set of 'cost' parameters. We demonstrate that the algorithm performs well when compared against existing methods. AVAILABILITY AND IMPLEMENTATION: The software is available at https://github.com/a-ignatieva/kwarg. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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.