Quartet Inference from SNP Data Under the Coalescent Model

By Julia Chifman, Laura Salter Kubatko. Bioinform., 2014

1,065 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting (2015, methodology): “This strategy is used in [42] to infer species trees under ILS.”
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, methodology): “Another quartet method is SVDquartets, which utilizes single-nucleotide polymorphism (SNP) matrices (Chifman and Kubatko 2014).”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, methodology): “We used the program SVDquartets v.1.0 (Chifman and Kubatko 2014) to estimate a species tree using the RAD loci.”
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, methodology): “In this article, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees.”
Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’ (2017, methodology): “An additional coalescent species tree was generated using svdquartets (Chifman & Kubatko, 2014) as implemented in © 2017 The Royal Entomological Society, Systematic Entomology, 42, 786–795 paup* v. 4 (Swofford, 2003).”