Amer, A., Galvin, S., Healy, C. M., & Moran, G. P. (2017). The microbiome of potentially malignant oral leukoplakia exhibits enrichment for fusobacterium, leptotrichia, campylobacter, and rothia species. Frontiers in Microbiology, 8, 2391.
Arenas, M. (2015). Trends in substitution models of molecular evolution. Frontiers in Genetics, 6.
Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C., & Segata, N. (2015). Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ, 3, e1029.
Barton, K., Hiener, B., Winckelmann, A., Rasmussen, T. A., Shao, W., Byth, K., Lanfear, R., Solomon, A., McMahon, J., Harrington, S., Buzon, M., Lichterfeld, M., Denton, P. W., Olesen, R., Østergaard, L., Tolstrup, M., Lewin, S. R., Søgaard, O. S., & Palmer, S. (2016). Broad activation of latent HIV-1 in vivo. Nature Communications, 7, 12731.
Berger, S. A., Krompass, D., & Stamatakis, A. (2011). Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood. Systematic Biology, 291–302.
Bosi, E., Monk, J. M., Aziz, R. K., Fondi, M., Nizet, V., & Palsson, B. Ø. (2016). Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proceedings of the National Academy of Sciences of the United States of America, 113(26), E3801–E3809.
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014). BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput Biol, 10(4), e1003537.
Boussau, B., Szöllősi, G. J., Duret, L., Gouy, M., Tannier, E., & Daubin, V. (2013). Genome-scale coestimation of species and gene trees. Genome Research, 23(2), 323–330.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583.
Chen, Z., Ho, W. C. S., Boon, S. S., Law, P. T. Y., Chan, M. C. W., DeSalle, R., Burk, R. D., & Chan, P. K. S. (2017). Ancient evolution and dispersion of human papillomavirus 58 variants. Journal of Virology, 91(21), e01285–17.
Chevenet, F., Brun, C., Bañuls, A.-L., Jacq, B., & Christen, R. (2006). TreeDyn: Towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics, 7, 439.
Chow, N. A., Muñoz, J. F., Gade, L., Berkow, E. L., Li, X., Welsh, R. M., Forsberg, K., Lockhart, S. R., Adam, R., Alanio, A., Alastruey-Izquierdo, A., Althawadi, S., Araúz, A. B., Ben-Ami, R., Bharat, A., Calvo, B., Desnos-Ollivier, M., Escandón, P., Gardam, D., … Cuomo, C. A. (2020). Tracing the evolutionary history and global expansion of candida auris using population genomic analyses. mBio, 11(2).
Czech, L., Huerta-Cepas, J., & Stamatakis, A. (2017). A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits. Molecular Biology and Evolution, 34(6), 1535–1542.
Escudero, M., & Wendel, J. F. (2020). The grand sweep of chromosomal evolution in angiosperms. New Phytologist, 228(3), 805–808.
Felsenstein, J. (1978). Cases in which Parsimony or Compatibility Methods will be Positively Misleading. Systematic Biology, 27(4), 401–410.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368–376.
Felsenstein, J. (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164–166.
Fitch, W. M. (1971). Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Systematic Zoology, 20(4), 406–416.
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A. J., … Zhang, J. (2004). Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology, 5(10), R80.
Goldman, N., & Yang, Z. (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11(5), 725–736.
Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., Prieto, K., Reyes, D., Bingham, A. M., Paul, L. M., Robles-Sikisaka, R., Oliveira, G., Pronty, D., Barcellona, C. M., Metsky, H. C., … Andersen, K. G. (2017). Genomic epidemiology reveals multiple introductions of zika virus into the united states. Nature, 546(7658), 401–405.
Gupta, A., & Sharma, V. K. (2015). Using the taxon-specific genes for the taxonomic classification of bacterial genomes. BMC Genomics, 16(1).
He, Y.-Q., Chen, L., Xu, W.-B., Yang, H., Wang, H.-Z., Zong, W.-P., Xian, H.-X., Chen, H.-L., Yao, X.-J., Hu, Z.-L., Luo, M., Zhang, H.-L., Ma, H.-W., Cheng, J.-Q., Feng, Q.-J., & Zhao, D.-J. (2013). Emergence, Circulation, and Spatiotemporal Phylogenetic Analysis of Coxsackievirus A6- and Coxsackievirus A10-Associated Hand, Foot, and Mouth Disease Infections from 2008 to 2012 in Shenzhen, China. Journal of Clinical Microbiology, 51(11), 3560–3566.
He, Z., Gharaibeh, R. Z., Newsome, R. C., Pope, J. L., Dougherty, M. W., Tomkovich, S., Pons, B., Mirey, G., Vignard, J., Hendrixson, D. R., & Jobin, C. (2019). Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut, 68(2), 289–300.
He, Z., Zhang, H., Gao, S., Lercher, M. J., Chen, W.-H., & Hu, S. (2016). Evolview v2: An online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Research, 44(W1), W236–241.
Höhna, S., Heath, T. A., Boussau, B., Landis, M. J., Ronquist, F., & Huelsenbeck, J. P. (2014). Probabilistic graphical model representation in phylogenetics. Systematic Biology, 63(5), 753–771.
Höhna, S., Landis, M. J., Heath, T. A., Boussau, B., Lartillot, N., Moore, B. R., Huelsenbeck, J. P., & Ronquist, F. (2016). RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language. Systematic Biology, 65(4), 726–736.
Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England), 17(8), 754–755.
Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology, 61(6), 1061–1067.
Jombart, T., Aanensen, D. M., Baguelin, M., Birrell, P., Cauchemez, S., Camacho, A., Colijn, C., Collins, C., Cori, A., Didelot, X., Fraser, C., Frost, S., Hens, N., Hugues, J., Höhle, M., Opatowski, L., Rambaut, A., Ratmann, O., Soubeyrand, S., … Ferguson, N. (2014). OutbreakTools: A new platform for disease outbreak analysis using the R software. Epidemics, 7, 28–34.
Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J.others. (2012). Genomic analysis identifies association of fusobacterium with colorectal carcinoma. Genome Research, 22(2), 292–298.
Kuczynski, J., Stombaugh, J., Walters, W. A., González, A., Caporaso, J. G., & Knight, R. (2011). Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.], CHAPTER, Unit10.7.
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874.
Kunin, V., & Hugenholtz, P. (2010). PyroTagger : A fast , accurate pipeline for analysis of rRNA amplicon pyrosequence data. The Open Journal, 1–8.
Lam, T. T.-Y., Hon, C.-C., Lemey, P., Pybus, O. G., Shi, M., Tun, H. M., Li, J., Jiang, J., Holmes, E. C., & Leung, F. C.-C. (2012). Phylodynamics of H5N1 avian influenza virus in Indonesia. Molecular Ecology, 21(12), 3062–3077.
Lam, T. T.-Y., Zhou, B., Wang, J., Chai, Y., Shen, Y., Chen, X., Ma, C., Hong, W., Chen, Y., Zhang, Y., Duan, L., Chen, P., Jiang, J., Zhang, Y., Li, L., Poon, L. L. M., Webby, R. J., Smith, D. K., Leung, G. M., … Zhu, H. (2015). Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature, 522(7554), 102–105.
Larsen, F. T., Bed’Hom, B., Guldbrandtsen, B., & Dalgaard, T. S. (2019). Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies. Molecular Immunology, 114, 216–225.
Lemmon, A. R., & Moriarty, E. C. (2004). The importance of proper model assumption in bayesian phylogenetics. Systematic Biology, 53(2), 265–277.
Letunic, I., & Bork, P. (2007). Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics, 23(1), 127–128.
Liang, H., Lam, T. T.-Y., Fan, X., Chen, X., Zeng, Y., Zhou, J., Duan, L., Tse, M., Chan, C.-H., Li, L., Leung, T.-Y., Yip, C.-H., Cheung, C.-L., Zhou, B., Smith, D. K., Poon, L. L.-M., Peiris, M., Guan, Y., & Zhu, H. (2014). Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China. Journal of Virology, JVI.01327–14.
Lott, S. C., Voß, B., Hess, W. R., & Steglich, C. (2015). CoVennTree: A new method for the comparative analysis of large datasets. Frontiers in Genetics, 6, 43.
Maddison, D. R., Swofford, D. L., Maddison, W. P., & Cannatella, D. (1997). Nexus: An Extensible File Format for Systematic Information. Systematic Biology, 46(4), 590–621.
Matsen, F. A., Hoffman, N. G., Gallagher, A., & Stamatakis, A. (2012). A Format for Phylogenetic Placements. PLOS ONE, 7(2), e31009.
Matsen, F. A., Kodner, R. B., & Armbrust, E. V. (2010). Pplacer: Linear time maximum-likelihood and bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11(1), 538.
McMurdie, P. J., & Holmes, S. (2013). Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PloS One, 8(4), e61217.
Michonneau, F., Brown, J. W., & Winter, D. J. (2016). Rotl: An r package to interact with the open tree of life data. Methods in Ecology and Evolution, 7(12), 1476–1481.
Morgan, X. C., Segata, N., & Huttenhower, C. (2013). Biodiversity and functional genomics in the human microbiome. Trends in Genetics, 29(1), 51–58.
Neher, R. A., Bedford, T., Daniels, R. S., Russell, C. A., & Shraiman, B. I. (2016). Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proceedings of the National Academy of Sciences, 113(12), E1701–E1709.
Page, R. D. M. (2002). Visualizing phylogenetic trees using TreeView. Current Protocols in Bioinformatics, Chapter 6, Unit 6.2.
Paradis, E., Claude, J., & Strimmer, K. (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20(2), 289–290.
Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2005). HyPhy: Hypothesis testing using phylogenies. Bioinformatics (Oxford, England), 21(5), 676–679.
R Core Team. (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing.
Rannala, B., & Yang, Z. (1996). Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. Journal of Molecular Evolution, 43(3), 304–311.
Retief, J. D. (2000). Phylogenetic analysis using PHYLIP. Methods in Molecular Biology (Clifton, N.J.), 132, 243–258.
Revell, L. J. (2012). Phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3(2), 217–223.
Sanderson, M. J. (2003). r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19(2), 301–302.
Schliep, K. P. (2011). Phangorn: Phylogenetic analysis in R. Bioinformatics, 27(4), 592–593.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., & Weber, C. F. (2009). Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23), 7537–7541.
Schmidt, H. A., Strimmer, K., Vingron, M., & Haeseler, A. von. (2002). TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics (Oxford, England), 18(3), 502–504.
Schön, I., Shearn, R., Martens, K., Koenders, A., & Halse, S. (2015). Age and origin of Australian Bennelongia (Crustacea, Ostracoda). Hydrobiologia, 750(1), 125–146.
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome Biology, 12(6), R60.
Shoemaker, J. S., & Fitch, W. M. (1989). Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Molecular Biology and Evolution, 6(3), 270–289.
Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312–1313.
Venkatesh, D., Poen, M. J., Bestebroer, T. M., Scheuer, R. D., Vuong, O., Chkhaidze, M., Machablishvili, A., Mamuchadze, J., Ninua, L., Fedorova, N. B., Halpin, R. A., Lin, X., Ransier, A., Stockwell, T. B., Wentworth, D. E., Kriti, D., Dutta, J., Bakel, H. van, Puranik, A., … Lewis, N. S. (2018). Avian influenza viruses in wild birds: Virus evolution in a multihost ecosystem. Journal of Virology, 92(15).
Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H., Maddison, W. P., Midford, P. E., Priyam, A., Sukumaran, J., Xia, X., & Stoltzfus, A. (2012). NeXML: Rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology, 61(4), 675–689.
Wang, L.-G., Lam, T. T.-Y., Xu, S., Dai, Z., Zhou, L., Feng, T., Guo, P., Dunn, C. W., Jones, B. R., Bradley, T., Zhu, H., Guan, Y., Jiang, Y., & Yu, G. (2020). Treeio: An r package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution, 37(2), 599–603.
Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. Springer.
Wilgenbusch, J. C., & Swofford, D. (2003). Inferring evolutionary trees with PAUP*. Current Protocols in Bioinformatics, Chapter 6, Unit 6.4.
Wilkinson, L., Wills, D., Rope, D., Norton, A., & Dubbs, R. (2005). The Grammar of Graphics (2nd edition). Springer.
Wong, V. K., Baker, S., Pickard, D. J., Parkhill, J., Page, A. J., Feasey, N. A., Kingsley, R. A., Thomson, N. R., Keane, J. A., Weill, F.-X., Edwards, D. J., Hawkey, J., Harris, S. R., Mather, A. E., Cain, A. K., Hadfield, J., Hart, P. J., Thieu, N. T. V., Klemm, E. J., … Dougan, G. (2015). Phylogeographical analysis of the dominant multidrug-resistant H58 clade of salmonella typhi identifies inter- and intracontinental transmission events [Journal Article]. Nature Genetics, 47(6), 632–639.
Wu, N., Yang, X., Zhang, R., Li, J., Xiao, X., Hu, Y., Chen, Y., Yang, F., Lu, N., Wang, Z.others. (2013). Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microbial Ecology, 66(2), 462–470.
Xu, S., Chen, M., Feng, T., Li, Z., Lang, Z., & Yu, G. (2021). Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Frontiers in Genetics, 12, 774846.
Xu, S., Dai, Z., Guo, P., Fu, X., Liu, S., Zhou, L., Tang, W., Feng, T., Chen, M., Zhan, L., Wu, T., Hu, E., Jiang, Y., Bo, X., & Yu, G. (2021). ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data. Molecular Biology and Evolution, 38(9), 4039–4042.
Yang, Z. (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8), 1586–1591.
Yang, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. Journal of Molecular Evolution, 39(3), 306–314.
Yu, G. (2020). Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 69(1), e96.
Yu, G., & He, Q.-Y. (2016). ReactomePA: An r/bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems, 12(2), 477–479.
Yu, G., Lam, T. T.-Y., Zhu, H., & Guan, Y. (2018). Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 35(12), 3041–3043.
Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T.-Y. (2017). Ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8(1), 28–36.
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012). clusterProfiler: An r package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology, 16(5), 284–287.
Yu, G., Wang, L.-G., & He, Q.-Y. (2015). ChIPseeker: An R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics, 31(14), 2382–2383.
Yu, G., Wang, L.-G., Yan, G.-R., & He, Q.-Y. (2015). DOSE: An r/bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics, 31(4), 608–609.
Zmasek, C. M., & Eddy, S. R. (2001). ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics, 17(4), 383–384.