RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Citations
9,474 citations
5,027 citations
Cites methods from "RAxML version 8: a tool for phyloge..."
...Maximum-likelihood phylogenetic trees of each taxonomic group, such as phyla, classes, orders or families, were generated from manually aligned 16S rRNA gene sequences using RAxML software [14]....
[...]
4,337 citations
Cites result from "RAxML version 8: a tool for phyloge..."
...For example, optimization of the model parameters for the LG4X model on the AA-data set took 1.9 min in IQ-TREE 2, 3 min in RAxML-NG, and 17.6 min in PhyML-mixtures....
[...]
...We compared our scheduling approach with the program ParGenes version 1.0.1 (Morel et al. 2019), which uses RAxMLNG for tree search and a more sophisticated scheduling algorithm....
[...]
...In addition to implementing existing mixture models, IQ-TREE 2 goes beyond the mixture models employed in PhyML-mixtures (Le et al. 2008) and RAxML-NG software (Kozlov et al. 2019), by allowing for user-defined mixture models using the “MIXfmodel1,. ....
[...]
...The speed of FastTree2 was accomplished at the cost of producing substantially worse trees than RAxML, PhyML, and IQ-TREE (Zhou et al. 2018)....
[...]
...IQ-TREE 2 exploits partial terraces to improve tree search under partitioned models and achieves up to 4.5- and 8-fold speedups compared with IQ-TREE 1 and RAxML, respectively (Chernomor et al. 2016)....
[...]
2,692 citations
Cites methods from "RAxML version 8: a tool for phyloge..."
...It can also extract the tree/branch/node-specific and other data from the analysis outputs of BEAST, EPA, HYPHY, PAML, PHYLODOG, PPLACER, R8S, RAXML and REVBAYES software, and allows using these data to annotate the tree....
[...]
...Non-standard analysis output files from various evolutionary biology software packages including BEAST (Bouckaert et al. 2014), EPA (Berger, Krompass& Stamatakis 2011), HYPHY (Pond, Frost & Muse 2005), PAML (Yang 2007), PHYLODOG (Bastien et al. 2013), PPLACER (Matsen, Kodner & Armbrust 2010), RAXML (Stamatakis 2014), REVBAYES (Sebastian et al. 2014) and R8S (Sanderson 2003) (Table 1) can also be parsed into S4 objects using functions read.beast, read.codeml_mlc, read.codeml, read.hyphy, read.jplace, read.nhx, read.paml_rst, read.phylip, read.raxml and read.r8s (Fig....
[...]
...Computer programs and R packages for molecular evolutionary analyses in which their specific data outputs can be directly parsed by GGTREE Programs Data that can be parsed APE (R package) Bootstrap values BEAST Any information (e.g. substitution rates, node ages, geographic states) stored in the node attributes in the nexus-formatted tree file PAML-BASEML Ancestral sequences (from rst file) PAML-CODEML Ancestral sequences (from rst file) dN, dS andx estimates (frommlc file) HYPHY Ancestral sequences (from the nexus-formatted tree file) PHANGORN (R package) Ancestral sequences RAXML Branch support values R8S Tree with branch in unit of time, rate and absolute substitution PPLACER Taxon placement information from jplace- formatted tree file EPA Taxon placement information from jplace- formatted tree file PHYLODOG Any information from theNHX-formatted tree file REVBAYES Any information from theNHX-formatted tree file © 2016 The Authors....
[...]
...…2011), HYPHY (Pond, Frost & Muse 2005), PAML (Yang 2007), PHYLODOG (Bastien et al. 2013), PPLACER (Matsen, Kodner & Armbrust 2010), RAXML (Stamatakis 2014), REVBAYES (Sebastian et al. 2014) and R8S (Sanderson 2003) (Table 1) can also be parsed into S4 objects using functions read.beast,…...
[...]
2,488 citations
References
14,847 citations
"RAxML version 8: a tool for phyloge..." refers background or methods in this paper
...Since the last RAxML paper (Stamatakis, 2006), it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community....
[...]
...RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood....
[...]
...RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogen- etic analyses of large datasets under maximum likelihood....
[...]
14,385 citations
"RAxML version 8: a tool for phyloge..." refers background in this paper
...Since the last RAxML paper (Stamatakis, 2006), it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community....
[...]
6,585 citations
"RAxML version 8: a tool for phyloge..." refers background in this paper
...Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores....
[...]
2,469 citations
"RAxML version 8: a tool for phyloge..." refers background in this paper
...In the following, I will present some of the most notable new features and extensions of RAxML....
[...]
2,351 citations
"RAxML version 8: a tool for phyloge..." refers background in this paper
...It can correct for ascertainment bias (Lewis, 2001) for all of the above data types....
[...]