BEST: Bayesian estimation of species trees under the coalescent model

By Liang Liu. Bioinform., 2008

401 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6abebbba187478af846916b0b37a6c52afc015c2

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In Genetics

In Molecular Biology

Citations in the corpus

Multi‐gene phylogenetic analysis of south‐east Asian pest members of the Bactrocera dorsalis species complex (Diptera: Tephritidae) does not support current taxonomy (2014, methodology): “…individual gene trees in this study were unresolved and therefore prevented the use of the speciestree software (e.g.,Ane et al. 2007; Liu 2008; Liu et al. 2009; Kubatko 2009; Kubatko et al. 2009; Heled and Drummond 2010; Than and Nakhleh 2009; Than et al. 2008; Huang et al. 2010;…”
ASTRAL: genome-scale coalescent-based species tree estimation (2014, methodology): “Other statistically consistent species-tree estimation methods include BEST (Liu, 2008) and *BEAST (Heled and Drummond, 2010), which co-estimate gene trees and species trees from input sequence alignments; however, these methods are extremely computationally intensive on datasets with (cid:2) 100…”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, methodology): “Thus, for species classifications, methods that use coalescent theory to jointly estimate gene trees and the species tree would be more appropriate (Liu and Pearl 2007; Liu 2008; Liu et al. 2008; Heled and Drummond 2010).”
Inferring Phylogenies from RAD Sequence Data (2012, methodology): “Other methods for reconstructing species trees from gene trees are prohibitively slow on large data sets (BEST; [43]), or have not been tested on data sets consisting of large amounts of missing data (*BEAST, STEM; [22,23]).”
Anchored hybrid enrichment for massively high-throughput phylogenomics. (2012, methodology): “The number of loci captured was sufﬁcient to phylogeny estimated using 32 genes in BEST was well supported on all branches, despite evidence of gene discordance”
Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture (2016, background): “Approaches vary in their implementation: many estimate species relationships using the coalescent process and can account for gene tree uncertainty (Liu, 2008; Kubatko, Carstens & Knowles, 2009; Heled & Drummond, 2010; Liu, Yu & Edwards, 2010) while others are based on statistical summaries of…”
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, methodology): “Key words: Incomplete lineage sorting, multi-species coalescent, quartet-based methods, ASTRAL, posterior probability, local support, branch length estimation.”
StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates (2016, methodology): “Given the current challenges of using large phylogenomic data sets with *BEAST there have been three broad alternatives available to researchers; concatenate sequences from multiple loci, use heuristic methods statistically consistent with the MSC, or choose a tractable subset of loci to use with a ”
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis (2010, methodology): “Several approaches now specifically account for the discordance between genes, such as MDC (Maddison, 1997), STEM (Kubatko et al., 2009), BEST (Liu, 2008) and *BEAST (Heled and Drummond, 2010).”
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, methodology): “Several methods have been developed to accommodate the variability among gene trees when estimating species trees [6-11].”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, methodology): “ Liu L (2008) BEST: Bayesian estimation of species trees under the coalescent model.”
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times (2015, methodology): “developed to perform inference under the multi-species coalescent (Rannala and Yang, 2003; Liu and Pearl, 2007; Liu, 2008; Heled and Drummond, 2010; Yang, 2015).”
Species Delimitation: A Decade After the Renaissance (2013, neutral): “This new theoretical framework allows prediction of the probability distribution of gene trees given the species tree, and consequently, several methods were developed for estimating species trees from a collection of multiple gene trees under different algorithms [64,65].”