MSCquartets

swMATH34523CRANMSCquartetsMaRDI QIDQ46232

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

John A. Rhodes, Jonathan D. Mitchell, Elizabeth S. Allman, Hector Banos

Last update: 27 October 2023

Copyright license: MIT license, File License

Software version identifier: 1.1.2, 1.0.5, 1.1.0, 1.1.1, 1.3.1, 1.3.2

Source code repository: https://github.com/cran/MSCquartets

Description

Methods for analyzing and using quartets displayed on a collection of gene trees, primarily to make inferences about the species tree or network under the multi-species coalescent model. These include quartet hypothesis tests for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>, simplex plots of quartet concordance factors as presented by Allman et al. (2020) <doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, and the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>. Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

Cites work

• Hypothesis testing near singularities and boundaries
• Gene tree discord, simplex plots, and statistical tests under the coalescent
• Topological Metrizations of Trees, and New Quartet Methods of Tree Inference
• Inferring Metric Trees from Weighted Quartets via an Intertaxon Distance
• NANUQ: a method for inferring species networks from gene trees under the coalescent model
• MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R

Related Items (7)

Identifiability of species network topologies from genomic sequences using the logDet distance ⋮ Classes of explicit phylogenetic networks and their biological and mathematical significance ⋮ Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes ⋮ Inferring metric trees from weighted quartets via an intertaxon distance ⋮ Identifiability of local and global features of phylogenetic networks from average distances ⋮ The tree of blobs of a species network: identifiability under the coalescent ⋮ Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods

This page was built for software: MSCquartets