ArticleBioinformatics (Oxford, England)2018
MASCOT: parameter and state inference under the marginal structured coalescent approximation.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Home is where the host is: evolutionary history of geographic spread, host switching and adaptive genomic signatures in two generalist group BMicrobial genomics · 2026Article
- SAASI: Sampling Aware Ancestral State Inference.Nature communications · 2026Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
- Ancestral state reconstruction with discrete characters using deep learning.bioRxiv : the preprint server for biology · 2026Article
- SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.Bioinformatics (Oxford, England) · 2026Article
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- Whole-genome sequencing reveals genetic diversity and transmission dynamics ofMicrobial genomics · 2026Article
- Glacial meltwater is associated with gene-specific diversification of metal resistance genes in high Arctic soil microbiomes.Frontiers in microbiology · 2026Article
- Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.PLoS pathogens · 2025Article
- The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion.G3 (Bethesda, Md.) · 2025Article
- Navigating Sampling Bias in Discrete Phylogeographic Analysis: Assessing the Performance of an Adjusted Bayes Factor.Molecular biology and evolution · 2025Article
- Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics.bioRxiv : the preprint server for biology · 2025Article
- When migration leaves a clean trace: Decoupling migration from coalescence in the structured serial coalescent.bioRxiv : the preprint server for biology · 2025Article
- Temporal reconstruction of aMicrobial genomics · 2025Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.bioRxiv : the preprint server for biology · 2025Article
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.PLoS computational biology · 2025Article
- Tracing SARS-CoV-2 clusters across local scales using genomic data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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Abstract
Motivation: The structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many sub-populations, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states. We showed that our approximation provides unbiased migration rate and population size estimates across a wide parameter range. Results: We extend this approach by providing a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree. We show that this algorithm is able to increase the probability attributed to the true sub-population of a node. Furthermore we use improved integration techniques, such that our method is now able to analyse larger datasets, including a H3N2 dataset with 433 sequences sampled from five different locations. Availability and implementation: The presented methods are part of the BEAST2 package MASCOT, the Marginal Approximation of the Structured COalescenT. This package can be downloaded via the BEAUti package manager. The source code is available at https://github.com/nicfel/Mascot.git. Supplementary information: Supplementary data are available at Bioinformatics online.
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