Likelihood-based tests of topologies in phylogenetics.

By Nick Goldman, Jon P. Anderson, Allen G. Rodrigo. Systematic Biology, 2000

1,100 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/e7bba8744b6e9989567708ac45513912d714b163

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Citations in the corpus

Molecular Studies and Phylogeography of Amazonian Tetrapods and their Relation to Geological and Climatic Models (2010, methodology): “Statistical tests of topology include the Wilcoxon signed-ranks test (Templeton 1983) under a parsimony framework, the Shimodaira–Hasegawa test (Shimodaira & Hasegawa 1999) under the maximum likelihood criterion, and the parametric bootstrap (Goldman et al. 2000).”
Phylogenetic analysis of Tylenchida Thorne, 1949 as inferred from D2 and D3 expansion fragments of the 28S rRNA gene sequences (2006, methodology): “It has been shown that the SH test is more appropriate than the KH test for comparing multiple trees (Goldman et al., 2000).”
Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy (2006, result): “Although we are not aware of studies that compare the performance of the Templeton test with other tests of topology, the SH test has been shown to be conservative ( Goldman et al. 2000, Buckley 2002) when compared to other methodologies used to test topologies.”
PACo: A Novel Procrustes Application to Cophylogenetic Analysis (2013, methodology): “[25,26,27,28], including a Procrustes-based technique [29] similar to the one described herein.”
Phylogenetic Relationships and Chromosome Number Evolution in Passiflora (2006, methodology): “A parametric bootstrap approach (SOWH test Swofford et al. 1996; Goldman et al. 2000) was utilized to determine whether single or multiple intron loss hypotheses were equally likely given our data.”
MITOCHONDRIAL DNA PHYLOGENY OF BABBLERS (TIMALIIDAE) (2003, neutral): “under the maximum-likelihood criterion (Goldman et al. 2000)”
Inferring Evolutionary Trees with PAUP* (2003, methodology): “Methods designed to do this—i.e., Templeton (1983), Kishino and Hasegawa (1989), and Shimodaira and Hasegawa (1999; see also Goldman et al., 2000) are also available in PAUP* and can be implemented using the options under the pscores and lscores commands.”
CONSEL: for assessing the confidence of phylogenetic tree selection (2001, methodology): “…(Felsenstein, 1985), the Kishino–Hasegawa (KH) test (Kishino and Hasegawa, 1989), the Shimodaira–Hasegawa (SH) test (Shimodaira and Hasegawa, 1999; Goldman et al., 2000), the Weighted Shimodaira–Hasegawa (WSH) test (Shimodaira, 1993, 1998; Shimodaira and Hasegawa, 1999; Buckley et al., 2001),…”
A rapid bootstrap algorithm for the RAxML Web servers. (2008, background): “Although RELLs can also be used for likelihoodbased tests of topologies (Goldman et al., 2000), Waddell et al.”