A rapid bootstrap algorithm for the RAxML Web servers.

By Alexandros Stamatakis, Paul Hoover, Jacques Rougemont. Systematic Biology, 2008

7,202 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/730543ef418a898cb94b5854b79ea35b082abf89

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Citations in the corpus

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, methodology): “For protein and rbcL data sets, the behavior of RBS was the closest to SBS, as it was intended in the RBS approximation algo-rithm (Stamatakis et al. 2008).”
Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, methodology): “…parts of the gene region can be excluded ii) Maximum likelihood analysis (ML) The ML trees are conducted using RAxML-HPC2 on XSEDE (8.2.8) (Stamatakis et al. 2008, Stamatakis 2014) in the ‘CIPRES Science Gateway platform’ (Miller et al. 2010) incorporating various models of evolution with…”
The beetle tree of life reveals that Coleoptera survived end‐Permian mass extinction to diversify during the Cretaceous terrestrial revolution (2015, neutral): “3.2) (Stamatakis, 2006; Stamatakis et al., 2008; Silvestro & Michalak, 2011).”
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes (2012, methodology): “An unrooted maximum likelihood analysis was performed for each alignment using the RaxML (49) server (http://phylobench.”
A molecular phylogeny of Graphidaceae (Ascomycota, Lecanoromycetes, Ostropales) including 428 species (2013, methodology): “…combined supermatrix were subjected to maximum likelihood search using the RAxML-HPC BlackBox 7.3.2 on the Cipres Gateway server (Stamatakis 2006, Stamatakis et al. 2005, 2008; Miller et al. 2010; http://www.phylo.org/portal2/login!input.action), with parametric bootstrapping generating 350…”
Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal (2011, positive): “The RAxML analysis was performed using the web-server program version 7.0.4 (Stamatakis et al., 2008) available at the CIPRES portal in San Diego (http:// www.phylo.org).”
Biogeography of the Monimiaceae (Laurales): a role for East Gondwana and long‐distance dispersal, but not West Gondwana (2010, methodology): “All tree searches relied on maximum likelihood (ML) as implemented in RAxML (Stamatakis, 2006; Stamatakis et al., 2008) and the GTR + G model with eight gamma rate categories and separate partitions for the nuclear and chloroplast data.”
Lineages in Nectriaceae: re-evaluating the generic status of Ilyonectria and allied genera (2014, methodology): “The ML analysis was done using RAxML (randomised axelerated (sic) maximum likelihood for high performance computing, Stamatakis et al., 2005, 2008) through the CIPRES website (http://www. phylo.org) to obtain a second measure of branch support.”
One stop shop: backbones trees for important phytopathogenic genera: I (2014) (2014, methodology): “…were performed for maximum parsimony in PAUP v. 4.0b10 (Swofford 2002), maximum likelihood in RAxML 7.4.2 Black Box or RAxMl GUI (Stamatakis 2006; Stamatakis et al. 2008), PhyML 3.0 (Guindon et al. 2010) or Bayesian inference in MrBayes v. 3.1.2 (Huelsenbeck and Ronquist 2001) as specified in…”
Towards a phylogenetic classification of reef corals: the Indo‐Pacific genera Merulina, Goniastrea and Scapophyllia (Scleractinia, Merulinidae) (2014, positive): “9 (Stamatakis 2006; Stamatakis et al. 2008) with the GTRGAMMA model and 50 random start-”
Austropuccinia : a new genus name for the myrtle rust Puccinia psidii placed within the redefined family Sphaerophragmiaceae (Pucciniales) (2017, methodology): “One thousand runs with distinct starting trees were completed using the rapid bootstrap (BS) algorithm of RAxML (Stamatakis et al. 2008).”
Genome-wide evidence for speciation with gene flow in Heliconius butterflies (2013, methodology): “RAxML (Stamatakis 2006; Ott et al. 2007; Stamatakis et al. 2008) was used with the GTRGAMMA model, and 100 bootstrap replicates were performed.”