Bayesian estimation of concordance among gene trees.

By Cécile Ané, Bret R. Larget, David A. Baum, Stacey D. Smith, Antonis Rokas. Molecular biology and evolution, 2006

486 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/cccfd38145b98ce0ef1a5cb6e82ebfe75bc62748

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Citations in the corpus

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, unknown): “Other approaches for combining multiple gene trees include supertree [16-18] and reconciliation [19-22] methods, which may capture important biological details through parameters without modelling it explicitly [23,24].”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, methodology): “We note, however, that BUCKy [103] does not make assumptions regarding the source of discordance among the estimates of gene trees and that Kubatko [105] recently proposed a species tree approach that incorporates hybridization.”
Inferring Phylogenies from RAD Sequence Data (2012, background): “Unfortunately, many multilocus methods (e.g., BUCKy; [21]) currently require complete data matrices, i.e., that all loci have been sequenced for all taxa.”
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, background): “For example, one can weight each gene tree quartet around a branch by its SH-like support, BS, or advanced measures like concordance (Ané et al. 2007).”
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments (2010, background): “[77,25,85-89]), this tree is incorrect: the real evolutionary history of these 8 yeast taxa is in fact the right-hand tree in Figure 9, with no monophyletic relationship between S.”
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics (2014, background): “The program BUCKy does not assume a single source of discordance (An e et al. 2007; Larget et al. 2010).”
Anchored hybrid enrichment for massively high-throughput phylogenomics. (2012, methodology): “Using the resulting posterior estimates, we performed a Bayesian concordance analysis using BUCKy (Ané et al. 2007).”
Integrative taxonomy, or iterative taxonomy? (2011, methodology): “BUCKy (Ane et al., 2007) and AUGIST (Oliver, 2008) use consensus methods, and both simultaneously accommodate the uncertainty in gene genealogies and providing measures of confidence in species tree estimates.”