MRBAYES: Bayesian inference of phylogenetic trees.
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Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html. Contact: johnh@brahms.biology.rochester.edu
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Under the independent-rate assumption, it is possible to infer phylogenies but not to estimate molecular rates or divergence times, because the individual contributions of rate and time cannot be separated.
“Under such an assumption, it is possible to infer phylogenies (e.g., [ 9, 10]), but not to estimate molecular rates or divergence times, because the individual contributions of rate and time to molecular evolution cannot be separated.”
From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [9]
Phylogenetic gene trees were built using MrBayes with the LG substitution model, model parameters estimated with ProtTest3, and simulations stopped after at least 1M iterations passed after split frequency between runs reached below 0.01.
“Phylogenetic gene trees were built using the MrBayes package (Bayesian inference) 61 modified to incorporate the LG substitution model.Model parameters were estimated using the ProtTest3 package 62 .MrBayes was set to run two sets of four Markov chains.The simulations were stopped once, at least 1 M iterations passed after split frequency between the two runs reached level lower than 0.01.”
From Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans (2014) · cites this paper as [61]
Methods for inferring latent phylogenetic trees are frustrated by long run times and poor scalability to large datasets.
“Methods for inferring these latent phylogenetic trees continue to be of substantial interest 92-94, but are frustrated by long run times and poor scalability to large datasets.”
From Learning the protein language: Evolution, structure, and function (2021) · cites this paper as [92]
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Cites
Monte Carlo sampling methods using Markov chains and their applications.
Hastings, W. K. (1970) · Biometrika · doi:10.1093/biomet/57.1.97 · Cited by 15,195 · see citing works
Reversible Jump Markov Chain Monte Carlo Computation and Bayesian Model Determination
Green, P. J. (1995) · Biometrika · doi:10.1093/biomet/82.4.711 · Cited by 5,941 · see citing works
Markov Chains for Exploring Posterior Distributions
Tierney, L. (1994) · The Annals of Statistics · doi:10.1214/aos/1176325750 · Cited by 3,513 · see citing works
Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
Rannala, B. H., & Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338839 · Cited by 1,751 · see citing works
Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees
Larget, B. R., & Simon, D. L. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026160 · Cited by 1,624 · see citing works
Huber, P. J. (1997) · Springer series in statistics · doi:10.1007/978-1-4612-0667-5_6 · Cited by 1,556 · see citing works
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
Yang, Z., & Rannala, B. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025811 · Cited by 1,274 · see citing works
(1991) · University of Minnesota Digital Conservancy (University of Minnesota) · Cited by 1,077 · see citing works
Estimating the pattern of nucleotide substitution
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076 · see citing works
Yang, Z. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040082 · Cited by 1,040 · see citing works
Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
Mau, B., Newton, M. A., & Larget, B. R. (1999) · Biometrics · doi:10.1111/j.0006-341x.1999.00001.x · Cited by 541 · see citing works
Nexus: An Extensible File Format for Systematic Information
Maddison, D. R., Swofford, D. L., & Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.4.590 · Cited by 515 · see citing works
Phylogenetic Tree Construction Using Markov Chain Monte Carlo
Li, S., Pearl, D. K., & Doss, H. (2000) · Journal of the American Statistical Association · doi:10.1080/01621459.2000.10474227 · Cited by 284 · see citing works
Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo
Mau, B., & Newton, M. A. (1997) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.1997.10474731 · Cited by 177 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- Mau,B. (1996) Bayesian phylogenetic inference via Markov chain Monte carlo methods, PhD Dissertation, University of Wiscon- sin, Madison.
- Swofford,D., Olsen,G., Waddell,P. and Hillis,D.M. (1996) Phyloge- netic inference. In Hillis, Moritz and Mable (eds), Molecular Systematics, 2nd edition.. Sinauer, Sunderland, MA, pp. 407- 511.
Cited by
Sorted by citations
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · see citing works
“This unrooted alternative to the molecular clock was first suggested by Felsenstein [10] and has formed the basis of all modern phylogenetic inference and is implemented in all major phylogenetic packages (e.g., PHYLIP [11], PAUP* [12], and MrBayes [ 9 ]).”
BackgroundMethodUltrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844 · see citing works
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Huelsenbeck, J. P., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001) · Science · doi:10.1126/science.1065889 · Cited by 2,737 · see citing works
Self-citationApproximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
Anisimova, M., & Gascuel, O. (2006) · Systematic Biology · doi:10.1080/10635150600755453 · Cited by 2,693 · see citing works
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921 · see citing works
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
Lartillot, N., & Philippe, H. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh112 · Cited by 1,516 · see citing works
Gregoretti, I., Lee, Y.-M., & Goodson, H. V. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.006 · Cited by 1,456 · see citing works
JmjC-domain-containing proteins and histone demethylation
Klose, R. J., Kallin, E. M., & Zhang, Y. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1945 · Cited by 1,290 · see citing works
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works
The Amphimedon queenslandica genome and the evolution of animal complexity
Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E. A., Mitros, T., Richards, G. S., Conaco, C., Dacre, M., Hellsten, U., et al. (2010) · Nature · doi:10.1038/nature09201 · Cited by 1,049 · see citing works
The yak genome and adaptation to life at high altitude
Qiu, Q., Zhang, G., Ma, T., Qian, W., Wang, J., Ye, Z., Cao, C., Hu, Q., Kim, J., Larkin, D. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2343 · Cited by 971 · see citing works
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes
Yoon, H. S., Hackett, J. D., Ciniglia, C., Pinto, G., & Bhattacharya, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh075 · Cited by 945 · see citing works
The fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834 · see citing works
Self-citationTheory-based Bayesian models of inductive learning and reasoning
Tenenbaum, J. B., Griffiths, T. L., & Kemp, C. (2006) · Trends in Cognitive Sciences · doi:10.1016/j.tics.2006.05.009 · Cited by 880 · see citing works
Lartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705 · see citing works
Computing Bayes factors using thermodynamic integration.
Lartillot, N., & Philippe, H. (2006) · Systematic Biology · doi:10.1080/10635150500433722 · Cited by 668 · see citing works
Evolutionary history and the effect of biodiversity on plant productivity
Cadotte, M. W., Cardinale, B. J., & Oakley, T. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805962105 · Cited by 653 · see citing works
Molecular mechanisms of seed dormancy
GRAEBER, K., NAKABAYASHI, K., MIATTON, E., LEUBNER‐METZGER, G., & SOPPE, W. J. J. (2012) · Plant, Cell & Environment · doi:10.1111/j.1365-3040.2012.02542.x · Cited by 640 · see citing works
A general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546 · see citing works
Highways of gene sharing in prokaryotes
Beiko, R. G., Harlow, T. J., & Ragan, M. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504068102 · Cited by 535 · see citing works
Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., Stryke, D., Bouquet, J., Somasekar, S., Linnen, J. M., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0220-9 · Cited by 558 · see citing works
The sheep genome illuminates biology of the rumen and lipid metabolism
Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J. F., Faraut, T., Wu, C., Muzny, D. M., Li, Y., Zhang, W., et al. (2014) · Science · doi:10.1126/science.1252806 · Cited by 514 · see citing works
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
Prud'homme, B., Gompel, N., Rokas, A., Kassner, V. A., Williams, T. M., Yeh, S.-D., True, J. R., & Carroll, S. B. (2006) · Nature · doi:10.1038/nature04597 · Cited by 507 · see citing works
Fry, B. G. (2005) · Genome Research · doi:10.1101/gr.3228405 · Cited by 486 · see citing works
Learning the protein language: Evolution, structure, and function
Bepler, T., & Berger, B. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.017 · Cited by 483 · see citing works
Subramanian, R. P., Wildschutte, J. H., Russo, C., & Coffin, J. M. (2011) · Retrovirology · doi:10.1186/1742-4690-8-90 · Cited by 439 · see citing works
Modeling compositional heterogeneity
Foster, P. G. (2004) · Systematic Biology · doi:10.1080/10635150490445779 · Cited by 474 · see citing works
Yoon, H. S., Hackett, J. D., & Bhattacharya, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.172234799 · Cited by 442 · see citing works
Angiosperm diversification through time
Magallón, S., & Castillo, A. (2009) · American Journal of Botany · doi:10.3732/ajb.0800060 · Cited by 439 · see citing works
Model Selection in Phylogenetics
Sullivan, J., & Joyce, P. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.36.102003.152633 · Cited by 412 · see citing works
Evolution and diversity of Rickettsiabacteria
Weinert, L. A., Werren, J. H., Aebi, A., Stone, G. N., & Jiggins, F. M. (2009) · BMC Biology · doi:10.1186/1741-7007-7-6 · Cited by 414 · see citing works
Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
Gavryushkina, A., Heath, T. A., Ksepka, D. T., Stadler, T., Welch, D., & Drummond, A. J. (2016) · Systematic Biology · doi:10.1093/sysbio/syw060 · Cited by 372 · see citing works
The importance of proper model assumption in bayesian phylogenetics.
Lemmon, A. R., & Moriarty, E. C. (2004) · Systematic Biology · doi:10.1080/10635150490423520 · Cited by 356 · see citing works
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416991111 · Cited by 324 · see citing works
Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
Zimmermann, J., Glöckner, G., Jahn, R., Enke, N., & Gemeinholzer, B. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12336 · Cited by 317 · see citing works
BLANK, C. E., & SÁNCHEZ‐BARACALDO, P. (2010) · Geobiology · doi:10.1111/j.1472-4669.2009.00220.x · Cited by 298 · see citing works
Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage
Hailer, F., Kutschera, V. E., Hallström, B. M., Klassert, D., Fain, S. R., Leonard, J. A., Arnason, U., & Janke, A. (2012) · Science · doi:10.1126/science.1216424 · Cited by 308 · see citing works
Ancient bacteria show evidence of DNA repair
Johnson, S. S., Hebsgaard, M. B., Christensen, T. R., Mastepanov, M., Nielsen, R., Munch, K., Brand, T., Gilbert, M. T. P., Zuber, M. T., Bunce, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706787104 · Cited by 292 · see citing works
Lerner, H. R. L., & Mindell, D. P. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.04.010 · Cited by 264 · see citing works
Ancient deuterostome origins of vertebrate brain signalling centres
Pani, A. M., Mullarkey, E. E., Aronowicz, J., Assimacopoulos, S., Grove, E. A., & Lowe, C. J. (2012) · Nature · doi:10.1038/nature10838 · Cited by 252 · see citing works
CRYPTIC SPECIATION IN THE COSMOPOLITAN AND CLONAL HUMAN PATHOGENIC FUNGUS ASPERGILLUS FUMIGATUS
Pringle, A., Baker, D. M., Platt, J. L., Wares, J. P., Latgé, J. P., & Taylor, J. W. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb01059.x · Cited by 267 · see citing works
Structured statistical models of inductive reasoning
Kemp, C., & Tenenbaum, J. B. (2009) · Psychological Review · doi:10.1037/a0014282 · Cited by 259 · see citing works
Dellaporta, S. L., Xu, A., Sagasser, S., Jakob, W., Moreno, M. A., Buss, L. W., & Schierwater, B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602076103 · Cited by 252 · see citing works
Marlow, H. Q., Srivastava, M., Matus, D. Q., Rokhsar, D., & Martindale, M. Q. (2009) · Developmental Neurobiology · doi:10.1002/dneu.20698 · Cited by 247 · see citing works
Parallel adaptations to high temperatures in the Archaean eon
Boussau, B., Blanquart, S., Necsulea, A., Lartillot, N., & Gouy, M. (2008) · Nature · doi:10.1038/nature07393 · Cited by 242 · see citing works
Eastman, J. M., Alfaro, M. E., Joyce, P., Hipp, A. L., & Harmon, L. J. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01401.x · Cited by 240 · see citing works
Bayesian Model Adequacy and Choice in Phylogenetics
Bollback, J. P. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004175 · Cited by 215 · see citing works
de Gruyter, J., Woudenberg, J. H. C., Aveskamp, M. M., Verkley, G. J. M., Groenewald, J. Z., & Crous, P. W. (2010) · Mycologia · doi:10.3852/09-240 · Cited by 237 · see citing works
The methane cycle in ferruginous Lake Matano
CROWE, S. A., KATSEV, S., LESLIE, K., STURM, A., MAGEN, C., NOMOSATRYO, S., PACK, M. A., KESSLER, J. D., REEBURGH, W. S., ROBERTS, J. A., et al. (2011) · Geobiology · doi:10.1111/j.1472-4669.2010.00257.x · Cited by 217 · see citing works
Branch-length prior influences Bayesian posterior probability of phylogeny.
Yang, Z., & Rannala, B. (2005) · Systematic Biology · doi:10.1080/10635150590945313 · Cited by 228 · see citing works
RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation
Liu, K., Linder, C. R., & Warnow, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027731 · Cited by 207 · see citing works
Relaxation of selective constraint on dog mitochondrial DNA following domestication
Björnerfeldt, S., Webster, M. T., & Vilà, C. (2006) · Genome Research · doi:10.1101/gr.5117706 · Cited by 203 · see citing works
Ho, S. Y. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi125 · Cited by 190 · see citing works
Gaither, M. R., Bowen, B. W., Bordenave, T.-R., Rocha, L. A., Newman, S. J., Gomez, J. A., van Herwerden, L., & Craig, M. T. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-189 · Cited by 191 · see citing works
“The ML tree topology was confirmed by neighbor-joining (NJ) and Bayesian Markov Chain Monte Carlo (MCMC) analysis using MEGA 4.0 [52] and MRBAYES 3.1.1 [ 53 ], respectively.”
MethodInfluentialA late methanogen origin for molybdenum-dependent nitrogenase
BOYD, E. S., ANBAR, A. D., MILLER, S., HAMILTON, T. L., LAVIN, M., & PETERS, J. W. (2011) · Geobiology · doi:10.1111/j.1472-4669.2011.00278.x · Cited by 161 · see citing works
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
Boothby, T. C., Tenlen, J. R., Smith, F. W., Wang, J. R., Patanella, K. A., Osborne Nishimura, E., Tintori, S. C., Li, Q., Jones, C. D., Yandell, M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510461112 · Cited by 172 · see citing works
Pinzón, J. H., Sampayo, E., Cox, E., Chauka, L. J., Chen, C. A., Voolstra, C. R., & LaJeunesse, T. C. (2013) · Journal of Biogeography · doi:10.1111/jbi.12110 · Cited by 169 · see citing works
Defining the Origins of the NOD-Like Receptor System at the Base of Animal Evolution
Lange, C., Hemmrich, G., Klostermeier, U. C., Lopez-Quintero, J. A., Miller, D. J., Rahn, T., Weiss, Y., Bosch, T. C. G., & Rosenstiel, P. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq349 · Cited by 150 · see citing works
Genomic inventory and expression of Sox and Fox genes in the cnidarian Nematostella vectensis
Magie, C. R., Pang, K., & Martindale, M. Q. (2005) · Development Genes and Evolution · doi:10.1007/s00427-005-0022-y · Cited by 158 · see citing works
Phylogeographic history of grey wolves in Europe
Pilot, M., Branicki, W., Jędrzejewski, W., Goszczyński, J., Jędrzejewska, B., Dykyy, I., Shkvyrya, M., & Tsingarska, E. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-104 · Cited by 158 · see citing works
Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana
Zou, C., Lehti-Shiu, M. D., Thomashow, M., & Shiu, S.-H. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000581 · Cited by 149 · see citing works
Extavour, C. G., Pang, K., Matus, D. Q., & Martindale, M. Q. (2005) · Evolution & Development · doi:10.1111/j.1525-142x.2005.05023.x · Cited by 144 · see citing works
Leininger, S., Adamski, M., Bergum, B., Guder, C., Liu, J., Laplante, M., Bråte, J., Hoffmann, F., Fortunato, S., Jordal, S., et al. (2014) · Nature Communications · doi:10.1038/ncomms4905 · Cited by 136 · see citing works
Clarke, J. A., & Middleton, K. M. (2008) · Systematic Biology · doi:10.1080/10635150802022231 · Cited by 137 · see citing works
Lu, L., Chen, Y., Wang, Z., Li, X., Chen, W., Tao, Z., Shen, J., Tian, Y., Wang, D., Li, G., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0652-y · Cited by 137 · see citing works
Origin of mitochondrial DNA diversity of domestic yaks
Guo, S., Savolainen, P., Su, J., Zhang, Q., Qi, D., Zhou, J., Zhong, Y., Zhao, X., & Liu, J. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-73 · Cited by 116 · see citing works
Dong, Y., Zhang, X., Xie, M., Arefnezhad, B., Wang, Z., Wang, W., Feng, S., Huang, G., Guan, R., Shen, W., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1606-1 · Cited by 116 · see citing works
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 · see citing works
Monroe, E. A., & Van Dolah, F. M. (2008) · Protist · doi:10.1016/j.protis.2008.02.004 · Cited by 93 · see citing works
Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia
Weiland, M. E.-L., McArthur, A. G., Morrison, H. G., Sogin, M. L., & Svärd, S. G. (2005) · International Journal for Parasitology · doi:10.1016/j.ijpara.2004.12.009 · Cited by 93 · see citing works
Molecular phylogeny of the benthic shallow-water octopuses (Cephalopoda: Octopodinae)
Guzik, M. T., Norman, M. D., & Crozier, R. H. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.05.009 · Cited by 86 · see citing works
Insights into the Origin of Metazoan Filopodia and Microvilli
Sebé-Pedrós, A., Burkhardt, P., Sánchez-Pons, N., Fairclough, S. R., Lang, B. F., King, N., & Ruiz-Trillo, I. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst110 · Cited by 84 · see citing works
AAV Ancestral Reconstruction Library Enables Selection of Broadly Infectious Viral Variants
Santiago-Ortiz, J., Ojala, D. S., Westesson, O., Weinstein, J. R., Wong, S. Y., Steinsapir, A., Kumar, S., Holmes, I., & Schaffer, D. V. (2015) · Gene Therapy · doi:10.1038/gt.2015.74 · Cited by 83 · see citing works
Ehrmann, I., Dalgliesh, C., Liu, Y., Danilenko, M., Crosier, M., Overman, L., Arthur, H. M., Lindsay, S., Clowry, G. J., Venables, J. P., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003474 · Cited by 82 · see citing works
Wang, Z., Shen, X., Liu, B., Su, J., Yonezawa, T., Yu, Y., Guo, S., Ho, S. Y. W., Vilà, C., Hasegawa, M., et al. (2010) · Journal of Biogeography · doi:10.1111/j.1365-2699.2010.02379.x · Cited by 79 · see citing works
Detecting the symplesiomorphy trap: A multigene phylogenetic analysis of terebelliform annelids
Zhong, M., Hansen, B., Nesnidal, M., Golombek, A., Halanych, K. M., & Struck, T. H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-369 · Cited by 73 · see citing works
Ferrareze, P. A. G., Franceschi, V. B., Mayer, A. D. M., Caldana, G. D., Zimerman, R. A., & Thompson, C. E. (2021) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2021.104941 · Cited by 82 · see citing works
Teacher, A. G., Thomas, J. A., & Barnes, I. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-214 · Cited by 60 · see citing works
The Genetic Impact of Translocations and Habitat Fragmentation in Chamois (Rupicapra) spp.
Crestanello, B., Pecchioli, E., Vernesi, C., Mona, S., Martínková, N., Janiga, M., Hauffe, H. C., & Bertorelle, G. (2009) · Journal of Heredity · doi:10.1093/jhered/esp053 · Cited by 60 · see citing works
Zeh, J. A., Bonilla, M. M., Su, E. J., Padua, M. V., Anderson, R. V., Kaur, D., Yang, D., & Zeh, D. W. (2012) · Global Change Biology · doi:10.1111/j.1365-2486.2012.02640.x · Cited by 57 · see citing works
A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates
Marron, A. O., Alston, M. J., Heavens, D., Akam, M., Caccamo, M., Holland, P. W. H., & Walker, G. (2013) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.2543 · Cited by 54 · see citing works
A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa
Erives, A., & Fritzsch, B. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.119.400951 · Cited by 49 · see citing works
Ngcamphalala, P. I., Lamb, J., & Mukaratirwa, S. (2020) · Journal of Helminthology · doi:10.1017/s0022149x19000130 · Cited by 46 · see citing works
Simion, P., Bekkouche, N., Jager, M., Quéinnec, E., & Manuel, M. (2015) · Zoology · doi:10.1016/j.zool.2014.06.004 · Cited by 46 · see citing works
Pérez-Pardal, L., Sánchez-Gracia, A., Álvarez, I., Traoré, A., Ferraz, J. B. S., Fernández, I., Costa, V., Chen, S., Tapio, M., Cantet, R. J. C., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-36444-7 · Cited by 45 · see citing works
Mas-y-Mas, S., Barbon, M., Teyssier, C., Déméné, H., Carvalho, J. E., Bird, L. E., Lebedev, A., Fattori, J., Schubert, M., Dumas, C., et al. (2016) · PLOS ONE · doi:10.1371/journal.pone.0165139 · Cited by 43 · see citing works
Katafuchi, T., Yasue, H., Osaki, T., & Minamino, N. (2009) · Peptides · doi:10.1016/j.peptides.2009.06.012 · Cited by 37 · see citing works
Reitzel, A. M., Pang, K., Ryan, J. F., Mullikin, J. C., Martindale, M. Q., Baxevanis, A. D., & Tarrant, A. M. (2011) · EvoDevo · doi:10.1186/2041-9139-2-3 · Cited by 36 · see citing works
Molecular phylogeny and diversity of Myanmar and Bhutan mithun based on mtDNA sequences
TANAKA, K., TAKIZAWA, T., MURAKOSHI, H., DORJI, T., NYUNT, M. M., MAEDA, Y., YAMAMOTO, Y., & NAMIKAWA, T. (2011) · Animal Science Journal · doi:10.1111/j.1740-0929.2010.00819.x · Cited by 30 · see citing works
Masek, M., Palata, V., Bray, T. C., & Bocak, L. (2015) · PLOS ONE · doi:10.1371/journal.pone.0123855 · Cited by 27 · see citing works
Natural history of SLC11 genes in vertebrates: tales from the fish world
Neves, J. V., Wilson, J. M., Kuhl, H., Reinhardt, R., Castro, L. F. C., & Rodrigues, P. N. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-106 · Cited by 24 · see citing works
Forcina, G., Guerrini, M., van Grouw, H., Gupta, B. K., Panayides, P., Hadjigerou, P., Al-Sheikhly, O. F., Awan, M. N., Khan, A. A., Zeder, M. A., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1500677112 · Cited by 24 · see citing works
Castillo, S., Srithayakumar, V., Meunier, V., & Kyle, C. J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012066 · Cited by 21 · see citing works
Dorji, T., Mannen, H., Namikawa, T., Inamura, T., & Kawamoto, Y. (2010) · Animal Genetics · doi:10.1111/j.1365-2052.2010.02033.x · Cited by 19 · see citing works
Babb, P. L., Fernandez-Duque, E., & Schurr, T. G. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.05.006 · Cited by 16 · see citing works
Chethana, C. S., Chowdappa, P., Biju, C. N., Praveena, R., & Sujatha, A. M. (2016) · European Journal of Plant Pathology · doi:10.1007/s10658-016-0931-9 · Cited by 14 · see citing works
van Meer, V., Pawęska, J. T., Swanepoel, R., Grobbelaar, A., & Bastos, A. D. (2024) · Pathogens · doi:10.3390/pathogens13030261 · Cited by 5 · see citing works
Early evolution of the LIM homeobox gene family
Srivastava, M., Larroux, C., Lu, D. R., Mohanty, K., Chapman, J., Degnan, B. M., & Rokhsar, D. S. (2010) · BMC Biology · doi:10.1186/1741-7007-8-4 · Cited by 1 · see citing works
- Authors
- Huelsenbeck, J. P., & Ronquist, F.
- Affiliations
- University of Rochester (US)
- Uppsala University (SE)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-08-01
- Volume
- 17
- Issue
- 8
- Pages
- 754-755
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2161444534
- Cited by
- 21,937
- References
- 14
- Citations by year
- 2026: 365 · 2025: 531 · 2024: 640 · 2023: 709 · 2022: 767 · 2021: 1031 · 2020: 919 · 2019: 858 · 2018: 922 · 2017: 962 · 2016: 988 · 2015: 1000 · 2014: 1120 · 2013: 1222 · 2012: 1320
- FWCI
- 123.27
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0075406)
- Division of Environmental Biology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Mathematics › Statistics and Probability › Markov Chains and Monte Carlo Methods
- Keywords
- MrBayes, Bayesian phylogenetics, phylogenetic tree estimation, Markov chain Monte Carlo, molecular phylogeny
- MeSH terms
- Algorithms, Bayes Theorem, Markov Chains, Phylogeny, Software, Computational Biology
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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.
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