Cited by 15,582Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsPlant Diversity and Evolution

The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Open access

Stamatakis, Alexandros·2006·Bioinformatics

Open this paper in CoChat — free account Open PDF

Abstract

UNLABELLED: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. AVAILABILITY: icwww.epfl.ch/~stamatak

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/bioinformatics/btl446

Cites

12 of 12 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

MrBayes 3: Bayesian phylogenetic inference under mixed models
Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 29,194
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,923
Obesity 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
Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion
Zwickl, D. J. (2006) · Texas ScholarWorks (Texas Digital Library) · Cited by 3,108
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Stamatakis, A., Ludwig, T. G., & Meier, H. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti191 · Cited by 1,429
Self-citation
Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat
Ley, R. E., Harris, J. K., Wilcox, J., Spear, J. R., Miller, S. R., Bebout, B. M., Maresca, J. A., Bryant, D. A., Sogin, M. L., & Pace, N. R. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3685-3695.2006 · Cited by 472
Phylogenetic models of rate heterogeneity: A high performance computing perspective
Stamatakis, A. (2006) · Cited by 303
Self-citation
Phylogenetic models of rate heterogeneity: a high performance computing perspective
Stamatakis, A. (2006) · IEEE International Parallel and Distributed Processing Symposium (IPDPS) · doi:10.1109/ipdps.2006.1639535 · Cited by 292
Self-citation
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
Hordijk, W., & Gascuel, O. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti713 · Cited by 213
Phylogenetic diversity and ecology of environmental Archaea
Robertson, C. E., Harris, J. K., Spear, J. R., & Pace, N. R. (2005) · Current Opinion in Microbiology · doi:10.1016/j.mib.2005.10.003 · Cited by 155

Flagged first, then by citations

Show all 12 references

Sorted by citations

Items 801–900 of 1,054

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill
Rodriguez‐R, L. M., Overholt, W. A., Hagan, C., Huettel, M., Kostka, J. E., & Konstantinidis, K. T. (2015) · The ISME Journal · doi:10.1038/ismej.2015.5 · Cited by 177
Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): Molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy
Durand, J.-D., Shen, K., Chen, W., Jamandre, B. W., Blel, H., Diop, K., Nirchio, M., León, F. J. G.-D., Whitfield, A. K., Chang, C.-W., et al. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.03.006 · Cited by 175
PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES
Cui, R., Schumer, M. E., Kruesi, K., Walter, R. B., Andolfatto, P., & Rosenthal, G. G. (2013) · Evolution · doi:10.1111/evo.12099 · Cited by 175
Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda
Rota‐Stabelli, O., Kayal, E., Gleeson, D. M., Daub, J., Boore, J. L., Telford, M. J., Pisani, D., Blaxter, M., & Lavrov, D. V. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq030 · Cited by 175
Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA
Lorenzi, J. C. C., Cohen, Y. Z., Cohn, L. B., Kreider, E. F., Barton, J. P., Learn, G. H., Oliveira, T. Y., Lavine, C. L., Horwitz, J. A., Settler, A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617789113 · Cited by 175
Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
Nobu, M. K., Dodsworth, J. A., Murugapiran, S. K., Rinke, C., Gies, E., Webster, G., Schwientek, P., Kille, P., Parkes, R. J., Sass, H., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.97 · Cited by 175
Ancestral protein reconstruction: techniques and applications
Merkl, R., & Sterner, R. (2015) · Biological Chemistry · doi:10.1515/hsz-2015-0158 · Cited by 174
Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)
Straub, S. C. K., Cronn, R., Edwards, C., Fishbein, M., & Liston, A. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt140 · Cited by 174
An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: A case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae)
Hamilton, C. A., Hendrixson, B. E., Brewer, M. S., & Bond, J. E. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.11.007 · Cited by 174
Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade
Thrash, J. C., Boyd, A., Huggett, M. J., Grote, J., Carini, P., Yoder, R. J., Robbertse, B., Spatafora, J. W., Rappé, M. S., & Giovannoni, S. J. (2011) · Scientific Reports · doi:10.1038/srep00013 · Cited by 174
An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin
Thiergart, T., Landan, G., Schenk, M., Dagan, T., & Martin, W. F. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs018 · Cited by 174
Revisiting Metarhizium and the description of new species from Thailand
Mongkolsamrit, S., Khonsanit, A., Thanakitpipattana, D., Tasanathai, K., Noisripoom, W., Lamlertthon, S., Himaman, W., Houbraken, J. A. M. P., Samson, R. A., & Luangsa-ard, J. J. (2020) · Studies in Mycology · doi:10.1016/j.simyco.2020.04.001 · Cited by 174
A revised evolutionary history of Poales: origins and diversification
Bouchenak‐Khelladi, Y., Muasya, A. M., & Linder, H. P. (2014) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12160 · Cited by 173
Identification and Characterization of Psychrotolerant Sporeformers Associated with Fluid Milk Production and Processing
Ivy, R. A., Ranieri, M. L., Martin, N. H., den Bakker, H. C., Xavier, B. M., Wiedmann, M., & Boor, K. J. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.06536-11 · Cited by 173
Phylogeny, Taxonomy, and Astounding Genetic Diversity of Glissomonadida ord. nov., The Dominant Gliding Zooflagellates in Soil (Protozoa: Cercozoa)
Howe, A. T., Bass, D., Vickerman, K., Chao, E. E. Y., & Cavalier‐Smith, T. (2009) · Protist · doi:10.1016/j.protis.2008.11.007 · Cited by 173
A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds
Gómez, J. P., Bravo, G. A., Brumfield, R. T., Tello, J. G., & Cadena, C. D. (2010) · Journal of Animal Ecology · doi:10.1111/j.1365-2656.2010.01725.x · Cited by 173
Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
Romiguier, J., Ranwez, V., Delsuc, F., Galtier, N., & Douzery, E. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst116 · Cited by 173
Molecular Epidemiology Reveals Long‐Term Changes in HIV Type 1 Subtype B Transmission in Switzerland
Kouyos, R. D., von Wyl, V., Yerly, S., Böni, J., Taffé, P., Shah, C., Bürgisser, P., Klimkait, T., Weber, R. K., Hirschel, B. J., et al. (2010) · The Journal of Infectious Diseases · doi:10.1086/651951 · Cited by 173
High Prevalence of Antibiotic-Resistant Mycoplasma genitalium in Nongonococcal Urethritis: The Need for Routine Testing and the Inadequacy of Current Treatment Options
Pond, M. J., Nori, A., Witney, A. A., Lopeman, R. C., Butcher, P. D., & Sadiq, S. T. (2013) · Clinical Infectious Diseases · doi:10.1093/cid/cit752 · Cited by 173
Trends in substitution models of molecular evolution
Arenas, M. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00319 · Cited by 175
An overview of extant conifer evolution from the perspective of the fossil record
Leslie, A. B., Beaulieu, J. M., Holman, G., Campbell, C. S., Mei, W., Raubeson, L. R., & Mathews, S. (2018) · American Journal of Botany · doi:10.1002/ajb2.1143 · Cited by 173
Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa
Sperling, E. A., Peterson, K. J., & Pisani, D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp148 · Cited by 172
Prokaryotic taxonomy in the sequencing era – the polyphasic approach revisited
Kämpfer, P., & Glaeser, S. P. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02615.x · Cited by 172
Comparative Genomics of Wolbachia and the Bacterial Species Concept
Ellegaard, K., Klasson, L., Näslund, K., Bourtzis, K., & Andersson, S. G. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003381 · Cited by 172
Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea)
Puillandre, N., Bouchet, P., Duda, T. F., Kauferstein, S., Kohn, A. J., Olivera, B. M., Watkins, M., & Meyer, C. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.05.023 · Cited by 172
The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies
Ghyselinck, J., Pfeiffer, S., Heylen, K., Sessitsch, A., & Vos, P. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071360 · Cited by 172
The onset of microbial associations in the coral Pocillopora meandrina
Apprill, A. M., Marlow, H. Q., Martindale, M. Q., & Rappé, M. S. (2009) · The ISME Journal · doi:10.1038/ismej.2009.3 · Cited by 172
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
Li, F., Villarreal, J. C., Kelly, S. L., Rothfels, C. J., Melkonian, M., Frangedakis, E., Ruhsam, M., Sigel, E. M., Der, J. P., Pittermann, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319929111 · Cited by 172
Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles
Thomson, R. C., & Shaffer, H. B. (2009) · Systematic Biology · doi:10.1093/sysbio/syp075 · Cited by 172
Endosymbiotic bacteria as a source of carotenoids in whiteflies
Sloan, D. B., & Moran, N. A. (2012) · Biology Letters · doi:10.1098/rsbl.2012.0664 · Cited by 172
Genome‐wide patterns of divergence and gene flow across a butterfly radiation
Nadeau, N. J., Martin, S. H., Kozak, K. M., Salazar, C. A., Dasmahapatra, K. K., Davey, J. W., Baxter, S. W., Blaxter, M., Mallet, J., & Jiggins, C. D. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05730.x · Cited by 172
Restructuring higher taxonomy using broad-scale phylogenomics: The living Ophiuroidea
O’Hara, T. D., Hugall, A. F., Thuy, B., Stöhr, S., & Martynov, A. V. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.12.006 · Cited by 172
Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes
Xu, C., Dong, W., Li, W., Lu, Y., Xie, X., Jin, X., Shi, J., He, K., & Suo, Z. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00015 · Cited by 172
Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets
Zeng, L., Zhang, N., Zhang, Q., Endress, P. K., Huang, J., & Mā, H. (2017) · New Phytologist · doi:10.1111/nph.14503 · Cited by 172
Recent and Rapid Speciation with Limited Morphological Disparity in the Genus Rattus
Rowe, K. C., Aplin, K. P., Baverstock, P. R., & Moritz, C. C. (2011) · Systematic Biology · doi:10.1093/sysbio/syq092 · Cited by 171
Phylogeny and origins of holoparasitism in Orobanchaceae
McNeal, J. R., Bennett, J. R., Wolfe, A. D., & Mathews, S. (2013) · American Journal of Botany · doi:10.3732/ajb.1200448 · Cited by 171
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid
Wong, V., Baker, S. G., Connor, T. R., Pickard, D., Page, A. J., Dave, J., Murphy, N., Holliman, R. E., Sefton, A. M., Millar, M. R., et al. (2016) · Nature Communications · doi:10.1038/ncomms12827 · Cited by 171
Fusarium graminearum: pathogen or endophyte of North American grasses?
Lofgren, L. A., LeBlanc, N., Certano, A. K., Nachtigall, J., LaBine, K. M., Riddle, J. M., Broz, K., Dong, Y., Bethan, B., Kafer, C. W., et al. (2017) · New Phytologist · doi:10.1111/nph.14894 · Cited by 171
Pan-vertebrate comparative genomics unmasks retrovirus macroevolution
Hayward, A., Cornwallis, C. K., & Jern, P. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414980112 · Cited by 169
Divergent evolution of oxidosqualene cyclases in plants
Xue, Z., Duan, L., Liu, D., Guo, J., Ge, S., Dicks, J. L., O’Maille, P. E., Osbourn, A., & Qi, X. (2011) · New Phytologist · doi:10.1111/j.1469-8137.2011.03997.x · Cited by 170
Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling
Wiens, J. J., & Tiu, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042925 · Cited by 170
Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade
Xi, Z., Wang, Y., Bradley, R. K., Sugumaran, M., Marx, C. J., Rest, J. S., & Davis, C. “. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003265 · Cited by 170
Functional and phylogenetic assembly in a Chinese tropical tree community across size classes, spatial scales and habitats
Yang, J., Zhang, G., Ci, X., Swenson, N. G., Cao, M., Sha, L., Li, J., Baskin, C. C., Slik, J. W. F., & Lin, L. (2013) · Functional Ecology · doi:10.1111/1365-2435.12176 · Cited by 170
Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs
Jörger, K. M., Norenburg, J. L., Wilson, N. G., & Schrödl, M. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-245 · Cited by 170
Captured retroviral envelope syncytin gene associated with the unique placental structure of higher ruminants
Cornelis, G., Heidmann, O., Degrelle, S. A., Vernochet, C., Lavialle, C., Letzelter, C., Bernard-Stoecklin, S., Hassanin, A., Mulot, B., Guillomot, M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215787110 · Cited by 170
Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169
Diversification of the Yellow-shouldered bats, Genus Sturnira (Chiroptera, Phyllostomidae), in the New World tropics
Velazco, P. M., & Patterson, B. D. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.04.016 · Cited by 169
Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences
Redmond, N. E., Morrow, C. C., THACKER, R. W., Díaz, M. C., Boury‐Esnault, N., Cárdenas, P., Hajdu, E., Lôbo‐Hajdu, G., PICTON, B. E., Pomponi, S. A., et al. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict078 · Cited by 169
A new mitofusin topology places the redox-regulated C terminus in the mitochondrial intermembrane space
Mattie, S., Riemer, J., Wideman, J. G., & McBride, H. M. (2017) · The Journal of Cell Biology · doi:10.1083/jcb.201611194 · Cited by 169
Capnodiaceae
Chomnunti, P., Schoch, C. L., Aguirre-Hudson, B., Ko, T. W. K., Hongsanan, S., Jones, E. B. G., Kodsueb, R., Phookamsak, R., Chukeatirote, E., Bahkali, A. H., et al. (2011) · Fungal Diversity · doi:10.1007/s13225-011-0145-6 · Cited by 169
RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
Seedorf, H., Kittelmann, S., Henderson, G., & Janssen, P. H. (2014) · PeerJ · doi:10.7717/peerj.494 · Cited by 168
Time to revisit polyphasic taxonomy
Vandamme, P. A. R., & Peeters, C. (2014) · Antonie van Leeuwenhoek · doi:10.1007/s10482-014-0148-x · Cited by 168
A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change
Wan, Y., Schwaninger, H. R., Baldo, A. M., Labate, J. A., Zhong, G., & Simon, C. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-141 · Cited by 168
Competition and phylogeny determine community structure in Müllerian co-mimics
Alexandrou, M. A., Oliveira, C., Maillard, M., McGill, R. A. R., Newton, J., Creer, S., & Taylor, M. I. (2010) · Nature · doi:10.1038/nature09660 · Cited by 168
Topological and Functional Characterization of an Insect Gustatory Receptor
Zhang, H., Anderson, A. R., Trowell, S., Luo, A., Xiang, Z., & Xia, Q. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024111 · Cited by 168
DO GEOLOGICAL OR CLIMATIC PROCESSES DRIVE SPECIATION IN DYNAMIC ARCHIPELAGOS? THE TEMPO AND MODE OF DIVERSIFICATION IN SOUTHEAST ASIAN SHREWS
Esselstyn, J. A., Timm, R. M., & Brown, R. M. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00743.x · Cited by 168
Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer
Moyes, A. B., Kueppers, L. M., Pett‐Ridge, J., Carper, D. L., Vandehey, N., O’Neil, J. P., & Frank, A. C. (2016) · New Phytologist · doi:10.1111/nph.13850 · Cited by 168
Biological Species Are Universal across Life’s Domains
Bobay, L., & Ochman, H. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx026 · Cited by 168
Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO 2 fixation pathway
Figueroa, I. A., Barnum, T. P., Somasekhar, P. Y., Carlström, C. I., Engelbrektson, A. L., & Coates, J. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715549114 · Cited by 168
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat
Mendoza, M. L. Z., Xiong, Z., Escalera‐Zamudio, M., Runge, A. K. W., Thézé, J., Streicker, D. G., Frank, H. K., Rubio, E. L., Liu, S., Ryder, O. A., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0476-8 · Cited by 168
Rapid Emergence of Multidrug Resistant, H58-Lineage Salmonella Typhi in Blantyre, Malawi
Feasey, N. A., Gaskell, K., Wong, V., Msefula, C., Selemani, G., Kumwenda, S., Allain, T. J., Mallewa, J., Kennedy, N., Bennett, A., et al. (2015) · PLOS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0003748 · Cited by 167
Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome
Hodkinson, B. P., Gottel, N., Schadt, C. W., & Lutzoni, F. M. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02560.x · Cited by 167
Parasitic plants have increased rates of molecular evolution across all three genomes
Bromham, L. D., Cowman, P. F., & Lanfear, R. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-126 · Cited by 167
Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation
Pan, G., Xu, J., Li, T., Xia, Q., Liu, S., Zhang, G., Li, S., Li, C., Liu, H., Yang, L., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-186 · Cited by 167
Understanding angiosperm diversification using small and large phylogenetic trees
Smith, S. A., Beaulieu, J. M., Stamatakis, A., & Donoghue, M. J. (2011) · American Journal of Botany · doi:10.3732/ajb.1000481 · Cited by 167
Self-citation
Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
Nagy, L. G., Ohm, R. A., Kovács, G. M., Floudas, D., Riley, R. W., Gácser, A., Sipiczki, M., Davis, J. M., Doty, S., de Hoog, S., et al. (2014) · Nature Communications · doi:10.1038/ncomms5471 · Cited by 169
Fumarole-Supported Islands of Biodiversity within a Hyperarid, High-Elevation Landscape on Socompa Volcano, Puna de Atacama, Andes
Costello, E. K., Halloy, S. R. P., Reed, S. C., Sowell, P., & Schmidt, S. K. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01469-08 · Cited by 167
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life
Figueras, A. J., Robledo, D., Corvelo, A., Hermida, M., Pereiro, P., Rubiolo, J. A., Gómez‐Garrido, J., Carreté, L., Bello, X., Gut, M., et al. (2016) · DNA Research · doi:10.1093/dnares/dsw007 · Cited by 167
Culturable mycobiota from Karst caves in China, with descriptions of 20 new species
Zhang, Z., Liu, F., Zhou, X. M., Liu, X. Z., Liu, S. J., & Cai, L. (2017) · Persoonia - Molecular Phylogeny and Evolution of Fungi · doi:10.3767/persoonia.2017.39.01 · Cited by 167
Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic
Guo, Q., Li, M., Wang, C., Guo, J., Jiang, X., Tan, J., Wu, S. V., Wang, P., Xiao, T., Zhou, M., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-96903-6 · Cited by 169
PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
Kocot, K. M., Citarella, M. R., Moroz, L. L., & Halanych, K. M. (2013) · Evolutionary Bioinformatics · doi:10.4137/ebo.s12813 · Cited by 166
The evolution of the placenta drives a shift in sexual selection in livebearing fish
Pollux, B. J. A., Meredith, R. W., Springer, M. S., Garland, T., & Reznick, D. N. (2014) · Nature · doi:10.1038/nature13451 · Cited by 166
Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
Lanza, V. F., de Toro, M., Garcillán-Barcia, M. P., Mora, A., Blanco, J., Coque, T. M., & de la Cruz, F. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004766 · Cited by 166
Preexisting CD8 + T-cell immunity to the H7N9 influenza A virus varies across ethnicities
Quiñones‐Parra, S. M., Grant, E. J., Loh, L., Nguyen, T. H. O., Campbell, K.-A., Tong, S. Y. C., Miller, A., Doherty, P. C., Vijaykrishna, D., Rossjohn, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322229111 · Cited by 166
Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation
Koch, H., Galushko, A., Albertsen, M., Schintlmeister, A., Gruber-Dorninger, C., Lücker, S., Pelletier, É., Paslier, D. L., Spieck, E., Richter, A. A., et al. (2014) · Science · doi:10.1126/science.1256985 · Cited by 166
Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders
Bidegaray‐Batista, L., & Arnedo, M. A. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-317 · Cited by 166
Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.
Muñoz, R., Rossello-Mora, R. A., & Amann, R. (2016) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2016.04.004 · Cited by 166
Diaporthe is paraphyletic
Gao, Y., Liu, F., Duan, W., Crous, P. W., & Cai, L. (2017) · IMA Fungus · doi:10.5598/imafungus.2017.08.01.11 · Cited by 166
Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei)
Schönhuth, S., Vukić, J., Šanda, R., Yang, L., & Mayden, R. L. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.06.026 · Cited by 166
Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?
Apprill, A. M., Robbins, J., Eren, A. M., Pack, A. A., Réveillaud, J., Mattila, D. K., Moore, M. J., Niemeyer, M. E., Moore, K. M. T., & Mincer, T. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090785 · Cited by 165
Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials
Cornelis, G., Vernochet, C., Carradec, Q., Souquère, S., Mulot, B., Catzeflis, F. M., Nilsson, M. A., Menzies, B. R., Renfree, M. B., Pierron, G., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1417000112 · Cited by 165
An integrated phylogenomic approach toward pinpointing the origin of mitochondria
Wang, Z., & Wu, M. (2015) · Scientific Reports · doi:10.1038/srep07949 · Cited by 165
A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data
Spring, S., Scheuner, C., Göker, M., & Klenk, H. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00281 · Cited by 165
Functional convergence of microbes associated with temperate marine sponges
Ribes, M., Jiménez, E., Yahel, G., López‐Sendino, P., Dı́ez, B., Massana, R., Sharp, J. H., & Coma, R. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02701.x · Cited by 165
Molecular phylogeny of Triatomini (Hemiptera: Reduviidae: Triatominae)
Justi, S. A., Russo, C., Mallet, J. R. D. S., Obara, M. T., & Galvão, C. (2014) · Parasites & Vectors · doi:10.1186/1756-3305-7-149 · Cited by 165
Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets
Zhou, X., Shen, X.-X., Hittinger, C. T., & Rokas, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx302 · Cited by 164
Evidence for a bacterial mechanism for group-specific social odors among hyenas
Theis, K. R., Schmidt, T. M., & Holekamp, K. E. (2012) · Scientific Reports · doi:10.1038/srep00615 · Cited by 164
Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae)
Buerki, S., Forest, F., Acevedo‐Rodríguez, P., Callmander, M. W., Nylander, J. A. A., Harrington, M. G., Sanmartín, I., Küpfer, P., & Álvarez, N. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.01.012 · Cited by 164
A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)
Sloan, D. B., Triant, D. A., Forrester, N. J., Bergner, L. M., Wu, M., & TAYLOR, D. R. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.12.004 · Cited by 164
A Rhodopsin-Guanylyl Cyclase Gene Fusion Functions in Visual Perception in a Fungus
Avelar, G. M., Schumacher, R. I., Zaini, P. A., Leonard, G., Richards, T. A., & Gomes, S. L. (2014) · Current Biology · doi:10.1016/j.cub.2014.04.009 · Cited by 164
Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins
Engel, P., Goepfert, A., Stanger, F. V., Harms, A., Schmidt, A., Schirmer, T., & Dehio, C. (2012) · Nature · doi:10.1038/nature10729 · Cited by 163
Detection and Identification of Fungi Intimately Associated with the Brown SeaweedFucus serratus
Zuccaro, A., Schoch, C. L., Spatafora, J. W., Kohlmeyer, J., Draeger, S., & Mitchell, J. I. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01158-07 · Cited by 163
Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification
Freudenstein, J. V., & Chase, M. W. (2015) · Annals of Botany · doi:10.1093/aob/mcu253 · Cited by 163
Spatiotemporal Diversification of the True Frogs (Genus Rana ): A Historical Framework for a Widely Studied Group of Model Organisms
Yuan, Z., Zhou, W., Chen, X., Poyarkov, N. A., Chen, H.-M., Jang‐Liaw, N., Chou, W.-H., Matzke, N. J., Iizuka, K., Min, M., et al. (2016) · Systematic Biology · doi:10.1093/sysbio/syw055 · Cited by 163
Rates of phenotypic and genomic evolution during the Cambrian explosion
Lee, M. S. Y., Soubrier, J., & Edgecombe, G. D. (2013) · Current Biology · doi:10.1016/j.cub.2013.07.055 · Cited by 162
Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication
Meyer, R. S., Karol, K. G., Little, D. P., Nee, M., & Litt, A. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.02.006 · Cited by 162
Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals
Meredith, R. W., Gatesy, J., Murphy, W. J., Ryder, O. A., & Springer, M. S. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000634 · Cited by 162
Evolution and Classification of Myosins, a Paneukaryotic Whole-Genome Approach
Sebé-Pedrós, A., Grau‐Bové, X., Richards, T. A., & Ruiz‐Trillo, I. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu013 · Cited by 162
Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life
Hamilton, C. A., Lemmon, A. R., Lemmon, E. M., & Bond, J. E. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0769-y · Cited by 163
Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)
Lodge, D. J., Padamsee, M., Matheny, P. B., Aime, M. C., Cantrell, S. A., Boertmann, D., Kovalenko, A. E., Vizzini, A., Dentinger, B. T. M., Kirk, P. M., et al. (2013) · Fungal Diversity · doi:10.1007/s13225-013-0259-0 · Cited by 161

Authors: Stamatakis, A.
Affiliations: École Polytechnique Fédérale de Lausanne (CH)
Corresponding author: Stamatakis, Alexandros
ORCID: Stamatakis, Alexandros
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2006-08-23
Volume: 22
Issue: 21
Pages: 2688-2690
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btl446
OpenAlex: W2168696662
Cited by: 15,582
References: 12
Citations by year: 2026: 198 · 2025: 337 · 2024: 418 · 2023: 480 · 2022: 628 · 2021: 841 · 2020: 918 · 2019: 993 · 2018: 1019 · 2017: 1078 · 2016: 1245 · 2015: 1338 · 2014: 1714 · 2013: 1292 · 2012: 1075
FWCI: 82.83
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc
Locations: Bioinformatics (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
reroDoc Digital Library (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords: maximum likelihood phylogenetic inference, large phylogenies, parallel computing, MPI, bootstrapping, software performance comparison, phylogenetics software
MeSH terms: Algorithms, Models, Genetic, Phylogeny, Sequence Homology, Nucleic Acid, Software, Species Specificity, Models, Statistical, Sequence Alignment, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks