RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

By Alexandros Stamatakis, Thomas Ludwig, Harald Meier. Bioinform., 2005

1,499 citations recorded by the source corpus.

Subfields: Ecological Modeling, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/db52ed7e90a96a2db9bdbedebc1007b9cf222ca9

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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): “However, the correlations we observed were not nearly as high as those reported for RAxML test data sets ( R 2 ranging from 0.85 to 0.98): for protein data sets, the linear correlation of SBS and RBS had slope S = 0.76 and R 2 = 0.66, whereas for rbcL data these were S = 0.92 and R 2 = 0.69.”
Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria (2012, methodology): “7 using the General Time Reversible model of nucleotide substitution [30,31].”
Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly (2010, methodology): “0.4 (Stamatakis et al., 2005) to bootstrap the dataset (250 replicates) on the CIPRES computer cluster (Cyberinfrastructure for Phylogenetic Research; San Diego Supercomputing Center) using the GTR + CAT model (Stamatakis, 2006).”
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, methodology): “, using RAxML [75] with a GTR+C model for nucleotide sequences and a LG+F+C model for protein sequences).”
A Large‐Scale Phylogeny of Polygonaceae Based on Molecular Data (2009, methodology): “The primers used were rbcL (Lledo et al. 1046 INTERNATIONAL JOURNAL OF PLANT SCIENCES 1998), matK (Johnson and Soltis 1994; Steele and Vilgalys 1994; Plunkett et al. 1996), ndhF (Olmstead and Sweere 1994), and ITS (White et al. 1990; Sun et al. 1994).”
Walking the thin line between Russula and Lactarius: the dilemma of Russula subsect. Ochricompactae. (2008, methodology): “118) of maximum likelihood bootstrapping (MLBS) with the GTRMIX model and gamma distribution conducted in RAxML-VI-HPC (RAxML-bs; Stamatakis et al., 2005).”
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite (2007, neutral): “TTG-10 [39]”
Multiple Sequence Alignment (2005, background): “, MrBayes [32] and BEAST [33, 34]), distance-based estimation (e.”
Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities (2007, methodology): “... program of PHYLIP 3.62 (Fig. 2f to k); (iii) an ARB parsimony insertion tree where we inserted the sequences into a tree containing 10,000 smallsubunit rRNA sequences (an augmented version of the ARB database described in reference 9), using the parsimony insertion tool of ARB (14), and then rem”
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…”
Evolution of Oviposition Techniques in Stick and Leaf Insects (Phasmatodea) (2018, neutral): “Exploratory RAxML analyses (Stamatakis et al., 2005) were executed on initial data sets including individual gene alignments to monitor potential contamination and assess gene performance, and on the combined data to assess terminal inclusion for constrained nodes in the divergence time analyses (se”
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, methodology): “…re-grafting positions are limited to only those within a certain distance from the pruning position (known as the “lazy subtree rearrangement”) (Stamatakis et al. 2005); and 2) if the re-grafting to a candidate position results in a substantially worse likelihood value, all branches further…”
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak (2014, background): “3 with the GTRΓ nucleotide substitution model (31).”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “Mixture trees, for example, are the result of supermatrix analyses in which alignments from multiple unlinked genomic regions are concatenated into a single matrix and analyzed using a model that assumes no recombination within the matrix (e.g., those employed in RAxML, MrBayes, etc.).”