Sequential importance sampling for multiresolution Kingman-Tajima coalescent counting
From MaRDI portal
Abstract: Statistical inference of evolutionary parameters from molecular sequence data relies on coalescent models to account for the shared genealogical ancestry of the samples. However, inferential algorithms do not scale to available data sets. A strategy to improve computational efficiency is to rely on simpler coalescent and mutation models, resulting in smaller hidden state spaces. An estimate of the cardinality of the state-space of genealogical trees at different resolutions is essential to decide the best modeling strategy for a given dataset. To our knowledge, there is neither an exact nor approximate method to determine these cardinalities. We propose a sequential importance sampling algorithm to estimate the cardinality of the space of genealogical trees under different coalescent resolutions. Our sampling scheme proceeds sequentially across the set of combinatorial constraints imposed by the data. We analyse the cardinality of different genealogical tree spaces on simulations to study the settings that favor coarser resolutions. We estimate the cardinality of genealogical tree spaces from mtDNA data from the 1000 genomes and a sample from a Melanesian population to illustrate the settings in which it is advantageous to employ coarser resolutions.
Recommendations
- Finding the best resolution for the Kingman-Tajima coalescent: theory and applications
- Computational inference beyond Kingman's coalescent
- Importance sampling on coalescent histories. II: Subdivided population models
- Importance sampling on coalescent histories. I
- scientific article; zbMATH DE number 1094270
Cites work
- A sequential importance sampling algorithm for generating random graphs with prescribed degrees
- An Efficient Sampling Algorithm for Network Motif Detection
- Bayesian phylogenetic inference using a combinatorial sequential Monte Carlo method
- Counting genealogical trees
- Efficient algorithms for inferring evolutionary trees
- Exact enumeration of cherries and pitchforks in ranked trees under the coalescent model
- Finding the best resolution for the Kingman-Tajima coalescent: theory and applications
- Full likelihood inference from the site frequency spectrum based on the optimal tree resolution
- Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies
- scientific article; zbMATH DE number 420886 (Why is no real title available?)
- scientific article; zbMATH DE number 3817476 (Why is no real title available?)
- scientific article; zbMATH DE number 1094276 (Why is no real title available?)
- scientific article; zbMATH DE number 2070281 (Why is no real title available?)
- Mathematics and computer science: coping with finiteness
- On the number of segregating sites in genetical models without recombination
- Phylogeny. Discrete and random processes in evolution
- Random generation of combinatorial structures from a uniform distribution
- Rare event simulation and counting problems
- ReCombinatorics. The algorithmics of ancestral recombination graphs and explicit phylogenetic networks. With contributions from Charles H. Langley, Yun S. Song and Yufeng Wu
- Sequential importance sampling for estimating the number of perfect matchings in bipartite graphs: an ongoing conversation with Laci
- Sequential Monte Carlo Methods for Statistical Analysis of Tables
- The ages of mutations in gene trees
- The sample size required in importance sampling
Cited in
(9)- Enumeration of binary trees compatible with a perfect phylogeny
- Finding the best resolution for the Kingman-Tajima coalescent: theory and applications
- Computational inference beyond Kingman's coalescent
- Stopping-time resampling and population genetic inference under coalescent models
- Importance sampling on coalescent histories. I
- An adjacent-swap Markov chain on coalescent trees
- An Efficient Coalescent Model for Heterochronously Sampled Molecular Data
- Scalable test of statistical significance for protein-DNA binding changes with insertion and deletion of bases in the genome
- An efficient algorithm for generating the internal branches of a Kingman coalescent
This page was built for publication: Sequential importance sampling for multiresolution Kingman-Tajima coalescent counting
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2194460)
