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RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Abstract
Motivation: The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining. Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa. Results: In this paper we present the latest release of our program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor. We compare RAxML-III to the currently fastest implementations for maximum likelihood and bayesian inference: PHYML and MrBayes. Whereas RAxML-III performs worse than PHYML and MrBayes on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values. Availability Supplementary information: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http://wwwbode.cs.tum/~stamatak Contact: stamatak@cs.tum.edu
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Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Cited by
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Self-citationGreengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
A Rapid Bootstrap Algorithm for the RAxML Web Servers
Stamatakis, A., Hoover, P., & Rougemont, J. (2008) · Systematic Biology · doi:10.1080/10635150802429642 · Cited by 7,028
Self-citationObesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
Chernomor, O., von Haeseler, A., & Minh, B. Q. (2016) · Systematic Biology · doi:10.1093/sysbio/syw037 · Cited by 2,252
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129
“Phylogenetic Classification of Cordyceps and the Clavicipitaceous Fungi”
Sung, G.-H., Hywel-Jones, N. L., Sung, J.-M., Luangsa-ard, J. J., Shrestha, B., & Spatafora, J. W. (2007) · Studies in Mycology · doi:10.3114/sim.2007.57.01 · Cited by 1,077
Srinivasan, S., Hoffman, N. G., Morgan, M. T., Matsen, F. A., Fiedler, T. L., Hall, R. W., Ross, F. J., McCoy, C. O., Bumgarner, R., Marrazzo, J. M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037818 · Cited by 673
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526
A new time tree reveals Earth history’s imprint on the evolution of modern birds
Claramunt, S., & Cracraft, J. (2015) · Science Advances · doi:10.1126/sciadv.1501005 · Cited by 383
Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils
Schirrmeister, B. E., Gugger, M., & Donoghue, P. C. J. (2015) · Palaeontology · doi:10.1111/pala.12178 · Cited by 304
The evolution of Ebola virus: Insights from the 2013-2016 epidemic
Holmes, E. C., Dudas, G., Rambaut, A., & Andersen, K. G. (2016) · Nature · doi:10.1038/nature19790 · Cited by 314
Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306
Deep metazoan phylogeny: When different genes tell different stories
Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W. E. G., Nickel, M., Schierwater, B., et al. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.01.010 · Cited by 254
Using RAxML to infer phylogenies
Stamatakis, A. (2015) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0614s51 · Cited by 243
Self-citationStrong mitochondrial DNA support for a Cretaceous origin of modern avian lineages
Brown, J. W., Rest, J. S., García-Moreno, J., Sorenson, M. D., & Mindell, D. P. (2008) · BMC Biology · doi:10.1186/1741-7007-6-6 · Cited by 236
Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
Ghai, R., Mizuno, C. M., Picazo, A., Camacho, A., & Rodriguez-Valera, F. (2013) · Scientific Reports · doi:10.1038/srep02471 · Cited by 224
Molecular phylogeny of choanoflagellates, the sister group to Metazoa
Carr, M., Leadbeater, B. S. C., Hassan, R., Nelson, M., & Baldauf, S. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801667105 · Cited by 205
Zhou, X., Shen, X.-X., Hittinger, C. T., & Rokas, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx302 · Cited by 164
Sperling, E. A., Peterson, K. J., & Pisani, D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp148 · Cited by 172
Paulk, N. K., Pekrun, K., Zhu, E., Nygaard, S., Li, B., Xu, J., Chu, K., Leborgne, C., Dane, A. P., Haft, A., et al. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2017.09.021 · Cited by 161
Carreté, L., Ksiezopolska, E., Pegueroles, C., Gómez-Molero, E., Saus, E., Iraola-Guzmán, S., Loska, D., Bader, O., Fairhead, C., & Gabaldón, T. (2018) · Current Biology · doi:10.1016/j.cub.2017.11.027 · Cited by 118
Takami, H., Noguchi, H., Takaki, Y., Uchiyama, I., Toyoda, A., Nishi, S., Chee, G.-J., Arai, W., Nunoura, T., Itoh, T., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030559 · Cited by 115
A Global Survey of Mycobacterial Diversity in Soil
Walsh, C. M., Gebert, M. J., Delgado-Baquerizo, M., Maestre, F. T., & Fierer, N. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.01180-19 · Cited by 111
Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites
Baker, A. J., Haddrath, O., McPherson, J. D., & Cloutier, A. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu153 · Cited by 108
Evolutionary genomics of yeast pathogens in the Saccharomycotina
Gabaldón, T., Naranjo-Ortíz, M. A., & Marcet-Houben, M. (2016) · FEMS Yeast Research · doi:10.1093/femsyr/fow064 · Cited by 105
Deciphering protein evolution and fitness landscapes with latent space models
Ding, X., Zou, Z., & Brooks III, C. L. (2019) · Nature Communications · doi:10.1038/s41467-019-13633-0 · Cited by 106
POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria
Wheeler, W. C., Lucaroni, N., Hong, L., Crowley, L. M., & Varón, A. (2015) · Cladistics · doi:10.1111/cla.12083 · Cited by 89
Detecting the Immune System Response of a 500 Year-Old Inca Mummy
Corthals, A., Koller, A., Martin, D. W., Rieger, R., Chen, E. I., Bernaski, M., Recagno, G., & Dávalos, L. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041244 · Cited by 65
Roure, B., & Philippe, H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-17 · Cited by 64
Cytological Characterization of YpsB, a Novel Component of the Bacillus subtilis Divisome
Tavares, J. R., de Souza, R. F., Meira, G. L. S., & Gueiros-Filho, F. J. (2008) · Journal of Bacteriology · doi:10.1128/jb.00064-08 · Cited by 51
Conserved meiotic genes point to sex in the Choanoflagellates
CARR, M., LEADBEATER, B. S. C., & BALDAUF, S. L. (2010) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2009.00450.x · Cited by 41
The mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37
Masek, M., Palata, V., Bray, T. C., & Bocak, L. (2015) · PLOS ONE · doi:10.1371/journal.pone.0123855 · Cited by 27
Genomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Resurrecting Golgi proteins to grasp Golgi ribbon formation and self-association under stress
Mendes, L. F. S., Batista, M. R. B., Kava, E., Bleicher, L., Micheletto, M. C., & Costa-Filho, A. J. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.11.173 · Cited by 13
Lineage-specific expansions provide genomic complexity among sea urchin GTPases
Beane, W. S., Voronina, E., Wessel, G. M., & McClay, D. R. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.046 · Cited by 10
Yan, Y., Wang, H., Li, D., Yang, X., Wang, Z., Qi, Z., Zhang, Q., Cui, B., Guo, Z., Yu, C., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085374 · Cited by 9
Metadata
- Authors
- Stamatakis, A., Ludwig, T., & Meier, H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-12-17
- Volume
- 21
- Issue
- 4
- Pages
- 456-463
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2117752525
- Cited by
- 1,438
- References
- 4
- FWCI
- 9.84
- Type
- journal article
- Language
- en
- Open access
- closed
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