Computational Inference Beyond Kingman's Coalescent

DOI10.1239/JAP/1437658613zbMath1347.60120arXiv1311.5699OpenAlexW2131649208MaRDI QIDQ2949852

Jere Koskela, Paul A. Jenkins, Dario Spanò

Publication date: 2 October 2015

Published in: Journal of Applied Probability (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1311.5699

zbMATH Keywords

importance samplingpopulation genetics\(\Lambda\)-coalescentconditional sampling distribution\(\Xi\)-coalescentapproximate conditionals

Mathematics Subject Classification ID

Sampling theory, sample surveys (62D05) Applications of branching processes (60J85) Branching processes (Galton-Watson, birth-and-death, etc.) (60J80) Genetics and epigenetics (92D10) Exchangeability for stochastic processes (60G09)

Related Items (5)

Full likelihood inference from the site frequency spectrum based on the optimal tree resolution ⋮ Asymptotic behaviour of sampling and transition probabilities in coalescent models under selection and parent dependent mutations ⋮ Multi-locus data distinguishes between population growth and multiple merger coalescents ⋮ Inference and rare event simulation for stopped Markov processes via reverse-time sequential Monte Carlo ⋮ A dual process for the coupled Wright-Fisher diffusion

Uses Software

• tsbridge

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Importance sampling for Lambda-coalescents in the infinitely many sites model
• Stopping-time resampling and population genetic inference under coalescent models
• A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms
• Analysis of DNA sequence variation within marine species using Beta-coalescents
• A sequentially Markov conditional sampling distribution for structured populations with migration and recombination
• On sampling distributions for coalescent processes with simultaneous multiple collisions
• Coalescent processes in subdivided populations subject to recurrent mass extinctions
• The coalescent
• Simulating probability distributions in the coalescent
• Coalescents with multiple collisions
• The ages of mutations in gene trees
• Coalescents with simultaneous multiple collisions
• Ancestral inference in population genetics
• Particle representations for measure-valued population models
• A classification of coalescent processes for haploid exchangeable population models
• Coalescent patterns in diploid exchangeable population models
• Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models
• Coalescent processes obtained from supercritical Galton-Watson processes.
• Importance Sampling for the Infinite Sites Model
• Importance sampling and the two-locus model with subdivided population structure
• A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks
• Inference in Molecular Population Genetics
• Importance sampling on coalescent histories. I
• Importance sampling on coalescent histories. II: Subdivided population models
• The general coalescent with asynchronous mergers of ancestral lines

This page was built for publication: Computational Inference Beyond Kingman's Coalescent