MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R

SUMMARY: MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus...

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Bibliographic Details
Published in:Bioinformatics
Main Authors: Rhodes, John A, Baños, Hector, Mitchell, Jonathan D, Allman, Elizabeth S
Format: Text
Language:English
Published: Oxford University Press 2020
Subjects:
Applications Notes
nanuq
Online Access:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289379/
http://www.ncbi.nlm.nih.gov/pubmed/33031510
https://doi.org/10.1093/bioinformatics/btaa868
Description
Summary:SUMMARY: MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. AVAILABILITY AND IMPLEMENTATION: MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets.

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