Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference

Evolutionary trees from DNA sequences: A maximum likelihood approach.

Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works

Likelihood Ratio Tests for Model Selection and Non-Nested Hypotheses

Vuong, Q. H. (1989) · Econometrica · doi:10.2307/1912557 · Cited by 5,929 · see citing works

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

Kishino, H., & Hasegawa, M. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02100115 · Cited by 3,378 · see citing works

Among-site rate variation and its impact on phylogenetic analyses

Yang, Z. (1996) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(96)10041-0 · Cited by 1,202 · see citing works

Further Results on Tests of Separate Families of Hypotheses

Cox, D. R. (1962) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/j.2517-6161.1962.tb00468.x · Cited by 1,037 · see citing works

Maximum likelihood inference of protein phylogeny and the origin of chloroplasts

Kishino, H., Miyata, T., & Hasegawa, M. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02109483 · Cited by 887 · see citing works

Mammalian phytogeny: shaking the tree

Novacek, M. J. (1992) · Nature · doi:10.1038/356121a0 · Cited by 641 · see citing works

Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA

Adachi, J., & Hasegawa, M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02498640 · Cited by 514 · see citing works

Phylogenetic position of the order Lagomorpha (rabbits, hares and allies)

Graur, D., Duret, L., & Gouy, M. (1996) · Nature · doi:10.1038/379333a0 · Cited by 294 · see citing works

Using Novel Phylogenetic Methods to Evaluate Mammalian mtDNA, Including Amino Acid-Invariant Sites-LogDet plus Site Stripping, to Detect Internal Conflicts in the Data, with Special Reference to the Positions of Hedgehog, Armadillo, and Elephant

Waddell, P. J., Cao, Y., Hauf, J., & Hasegawa, M. (1999) · Systematic Biology · doi:10.1080/106351599260427 · Cited by 171 · see citing works

Testing Hypotheses of Chaetognath Origins: Long Branches Revealed by 18S Ribosomal DNA

Halanych, K. M. (1996) · Systematic Biology · doi:10.1093/sysbio/45.2.223 · Cited by 92 · see citing works

A test whether two AIC'S differ significantly

Linhart, H. (1988) · South African Statistical Journal · Cited by 62 · see citing works

Phylogenetic position of cetaceans relative to artiodactyls: reanalysis of mitochondrial and nuclear sequences

Hasegawa, M., & Adachi, J. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025632 · Cited by 45 · see citing works

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376 · see citing works

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873 · see citing works

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

Ultrafast 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

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Posada, D., & Buckley, T. R. (2004) · Systematic Biology · doi:10.1080/10635150490522304 · Cited by 3,927 · see citing works

An approximately unbiased test of phylogenetic tree selection

Shimodaira, H. (2002) · Systematic Biology · doi:10.1080/10635150290069913 · Cited by 2,791 · see citing works

Tunicates and not cephalochordates are the closest living relatives of vertebrates

Delsuc, F., Brinkmann, H., Chourrout, D., & Philippe, H. (2006) · Nature · doi:10.1038/nature04336 · Cited by 1,651 · see citing works

Evolutionary analysis of <i>Arabidopsis</i> , cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T., Leister, D., Stoebe, B., Hasegawa, M., & Penny, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.182432999 · Cited by 1,178 · see citing works

The ctenophore genome and the evolutionary origins of neural systems

Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Grigorenko, A. P., Dailey, C., Berezikov, E., Buckley, K. M., et al. (2014) · Nature · doi:10.1038/nature13400 · Cited by 716 · see citing works

Genome-scale phylogeny and the detection of systematic biases.

Phillips, M. J., Delsuc, F., & Penny, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh137 · Cited by 450 · see citing works

A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis

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

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

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

Medina, M., Collins, A. G., Silberman, J. D., & Sogin, M. L. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171316998 · Cited by 395 · see citing works

Evolutionary Origins of Genomic Repertoires in Bacteria

Lerat, E., Daubin, V., Ochman, H., & Moran, N. A. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030130 · Cited by 338 · see citing works

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

Schierwater, B., Eitel, M., Jakob, W., Osigus, H.-J., Hadrys, H., Dellaporta, S. L., Kolokotronis, S.-O., & DeSalle, R. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000020 · Cited by 260 · see citing works

Model misspecification and probabilistic tests of topology: evidence from empirical data sets.

Buckley, T. R. (2002) · Systematic Biology · doi:10.1080/10635150290069922 · Cited by 253 · see citing works

Using RAxML to infer phylogenies

Stamatakis, A. (2015) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0614s51 · Cited by 243 · see citing works

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Fabre, P. H., Rodrigues, A., & Douzery, E. J. P. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.004 · Cited by 211 · see citing works

Deep Phylogeny and Evolution of Sponges (Phylum Porifera)

Wörheide, G., Dohrmann, M., Erpenbeck, D., Larroux, C., Maldonado, M., Voigt, O., Borchiellini, C., & Lavrov, D. V. (2012) · Advances in Marine Biology · doi:10.1016/b978-0-12-387787-1.00007-6 · Cited by 166 · see citing works

TreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information

Struck, T. H. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s14239 · Cited by 128 · see citing works

The molecular population genetics of HIV-1 group O.

Lemey, P., Pybus, O. G., Rambaut, A., Drummond, A. J., Robertson, D. L., Roques, P., Worobey, M., & Vandamme, A.-M. (2004) · Genetics · doi:10.1534/genetics.104.026666 · Cited by 131 · see citing works

Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria

Muñoz-Gómez, S. A., Susko, E., Williamson, K., Eme, L., Slamovits, C. H., Moreira, D., López-García, P., & Roger, A. J. (2022) · Nature Ecology &amp; Evolution · doi:10.1038/s41559-021-01638-2 · Cited by 111 · see citing works

A fully resolved genus level phylogeny of neotropical primates (Platyrrhini)

Wildman, D. E., Jameson, N. M., Opazo, J. C., & Yi, S. V. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.07.019 · Cited by 122 · see citing works

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.

Matsui, A., Rakotondraparany, F., Munechika, I., Hasegawa, M., & Horai, S. (2009) · Gene · doi:10.1016/j.gene.2008.08.024 · Cited by 121 · see citing works

Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP.

Poux, C., & Douzery, E. J. P. (2004) · American Journal of Physical Anthropology · doi:10.1002/ajpa.10322 · Cited by 103 · see citing works

Grazers, shredders and filtering carnivores—The evolution of feeding ecology in Drusinae (Trichoptera: Limnephilidae): Insights from a molecular phylogeny

Pauls, S. U., Graf, W., Haase, P., Lumbsch, H. T., & Waringer, J. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.11.003 · Cited by 92 · see citing works

Genome Networks Root the Tree of Life between Prokaryotic Domains

Dagan, T., Roettger, M., Bryant, D., & Martin, W. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq025 · Cited by 87 · 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

Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae)

do Amaral, F. R., Sheldon, F. H., Gamauf, A., Haring, E., Riesing, M., Silveira, L. F., & Wajntal, A. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.07.020 · Cited by 69 · see citing works

Likelihood Calculation in Molecular Phylogenetics

Bryant, D., Galtier, N., & Poursat, M.-A. (2005) · Mathematics of Evolution and Phylogeny · doi:10.1093/oso/9780198566106.003.0002 · Cited by 57 · see citing works

Response of the human gut and saliva microbiome to urbanization in Cameroon

Lokmer, A., Aflalo, S., Amougou, N., Lafosse, S., Froment, A., Tabe, F. E., Poyet, M., Groussin, M., Said-Mohamed, R., & Ségurel, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-59849-9 · Cited by 46 · see citing works

Automation and evaluation of the SOWH Test with SOWHAT

Church, S. H., Ryan, J. F., & Dunn, C. W. (2015) · Systematic Biology · doi:10.1093/sysbio/syv055 · Cited by 50 · see citing works

A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene

Johnston, A. R., & Anthony, N. M. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-120 · Cited by 36 · see citing works

Species boundaries and evolutionary lineages in the blue green damselfishes <i>Chromis viridis </i>and <i>Chromis atripectoralis </i>(Pomacentridae)

Froukh, T., & Kochzius, M. (2008) · Journal of Fish Biology · doi:10.1111/j.1095-8649.2007.01746.x · Cited by 32 · see citing works

A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta)

Onyshchenko, A., Ruck, E. C., Nakov, T., & Alverson, A. J. (2019) · American Journal of Botany · doi:10.1002/ajb2.1267 · Cited by 18 · see citing works

U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals

Jin, Y., & Qian, H. (2022) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2022.12.007 · Cited by 194 · see citing works

Effect of co-evolving amino acid residues on topology of phylogenetic trees

Sherbakov, D. Y., & Triboy, T. I. (2007) · Biochemistry (Moscow) · doi:10.1134/s0006297907120103 · Cited by 3 · see citing works

A survey on topologies of multilevel converters and study of two novel topologies

Wang, C., & Li, Y. (2009) · doi:10.1109/ipemc.2009.5157505 · Cited by 24 · see citing works

BIMLR: A method for constructing rooted phylogenetic networks from rooted phylogenetic trees

Wang, J., Guo, M., Xing, L., et al. (2013) · Gene · doi:10.1016/j.gene.2013.06.036 · Cited by 12 · see citing works

Phylogenetic Signal in the Eukaryotic Tree of Life

Sanderson, M. J. (2008) · Science · doi:10.1126/science.1154449 · Cited by 52 · see citing works