References

Amer, Abdrazak, Sheila Galvin, Claire M Healy, and Gary P Moran. 2017. “The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species.” Frontiers in Microbiology 8: 2391. https://doi.org/10.3389/fmicb.2017.02391.

Asnicar, Francesco, George Weingart, Timothy L Tickle, Curtis Huttenhower, and Nicola Segata. 2015. “Compact Graphical Representation of Phylogenetic Data and Metadata with Graphlan.” PeerJ 3: e1029. https://doi.org/10.7717/peerj.1029.

Berger, Simon A., Denis Krompass, and Alexandros Stamatakis. 2011. “Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads Under Maximum Likelihood.” Systematic Biology, March, 291–302. https://doi.org/10.1093/sysbio/syr010.

Bosi, Emanuele, Jonathan M. Monk, Ramy K. Aziz, Marco Fondi, Victor Nizet, and Bernhard Ø. Palsson. 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. https://doi.org/10.1073/pnas.1523199113.

Bouckaert, Remco, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, and Alexei J. Drummond. 2014. “BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.” PLoS Comput Biol 10 (4): e1003537. https://doi.org/10.1371/journal.pcbi.1003537.

Boussau, Bastien, Gergely J. Szöllősi, Laurent Duret, Manolo Gouy, Eric Tannier, and Vincent Daubin. 2013. “Genome-Scale Coestimation of Species and Gene Trees.” Genome Research 23 (2): 323–30. https://doi.org/10.1101/gr.141978.112.

Callahan, Benjamin J., Paul J. McMurdie, Michael J. Rosen, Andrew W. Han, Amy Jo A. Johnson, and Susan P. Holmes. 2016. “DADA2: High-Resolution Sample Inference from Illumina Amplicon Data.” Nature Methods 13 (7): 581–83. https://doi.org/10.1038/nmeth.3869.

Chen, Zigui, Wendy C. S. Ho, Siaw Shi Boon, Priscilla T. Y. Law, Martin C. W. Chan, Rob DeSalle, Robert D. Burk, and Paul K. S. Chan. 2017. “Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants.” Journal of Virology 91 (21): e01285–17. https://doi.org/10.1128/JVI.01285-17.

Chevenet, François, Christine Brun, Anne-Laure Bañuls, Bernard Jacq, and Richard Christen. 2006. “TreeDyn: Towards Dynamic Graphics and Annotations for Analyses of Trees.” BMC Bioinformatics 7 (October): 439. https://doi.org/10.1186/1471-2105-7-439.

Chow, Nancy A., José F. Muñoz, Lalitha Gade, Elizabeth L. Berkow, Xiao Li, Rory M. Welsh, Kaitlin Forsberg, et al. 2020. “Tracing the Evolutionary History and Global Expansion of Candida Auris Using Population Genomic Analyses.” Edited by Geraldine Butler and Kirsten Nielsen. mBio 11 (2). https://doi.org/10.1128/mBio.03364-19.

Felsenstein, J. 1981. “Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach.” Journal of Molecular Evolution 17 (6): 368–76.

Felsenstein, Joseph. 1989. “PHYLIP - Phylogeny Inference Package (Version 3.2).” Cladistics 5: 164–66.

———. 1978. “Cases in Which Parsimony or Compatibility Methods Will Be Positively Misleading.” Systematic Biology 27 (4): 401–10. https://doi.org/10.1093/sysbio/27.4.401.

Fitch, Walter M. 1971. “Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology.” Systematic Zoology 20 (4): 406–16. https://doi.org/10.2307/2412116.

Gentleman, Robert C, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, et al. 2004. “Bioconductor: Open Software Development for Computational Biology and Bioinformatics.” Genome Biology 5 (10): R80. https://doi.org/10.1186/gb-2004-5-10-r80.

Goldman, N., and Z. Yang. 1994. “A Codon-Based Model of Nucleotide Substitution for Protein-Coding DNA Sequences.” Molecular Biology and Evolution 11 (5): 725–36.

Grubaugh, Nathan D., Jason T. Ladner, Moritz U. G. Kraemer, Gytis Dudas, Amanda L. Tan, Karthik Gangavarapu, Michael R. Wiley, et al. 2017. “Genomic Epidemiology Reveals Multiple Introductions of Zika Virus into the United States.” Nature 546 (7658): 401–5. https://doi.org/10.1038/nature22400.

Gupta, Ankit, and Vineet K Sharma. 2015. “Using the Taxon-Specific Genes for the Taxonomic Classification of Bacterial Genomes.” BMC Genomics 16 (1). https://doi.org/10.1186/s12864-015-1542-0.

He, Ya-Qing, Long Chen, Wen-Bo Xu, Hong Yang, Han-Zhong Wang, Wen-Ping Zong, Hui-Xia Xian, et al. 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): 3560–6. https://doi.org/10.1128/JCM.01231-13.

He, Zhen, Raad Z Gharaibeh, Rachel C Newsome, Jllian L Pope, Michael W Dougherty, Sarah Tomkovich, Benoit Pons, et al. 2019. “Campylobacter Jejuni Promotes Colorectal Tumorigenesis Through the Action of Cytolethal Distending Toxin.” Gut 68 (2): 289–300. https://doi.org/10.1136/gutjnl-2018-317200.

He, Zilong, Huangkai Zhang, Shenghan Gao, Martin J. Lercher, Wei-Hua Chen, and Songnian Hu. 2016. “Evolview V2: An Online Visualization and Management Tool for Customized and Annotated Phylogenetic Trees.” Nucleic Acids Research 44 (W1): W236–241. https://doi.org/10.1093/nar/gkw370.

Höhna, Sebastian, Tracy A. Heath, Bastien Boussau, Michael J. Landis, Fredrik Ronquist, and John P. Huelsenbeck. 2014. “Probabilistic Graphical Model Representation in Phylogenetics.” Systematic Biology 63 (5): 753–71. https://doi.org/10.1093/sysbio/syu039.

Höhna, Sebastian, Michael J. Landis, Tracy A. Heath, Bastien Boussau, Nicolas Lartillot, Brian R. Moore, John P. Huelsenbeck, and Fredrik Ronquist. 2016. “RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.” Systematic Biology 65 (4): 726–36. https://doi.org/10.1093/sysbio/syw021.

Huelsenbeck, J. P., and F. Ronquist. 2001. “MRBAYES: Bayesian Inference of Phylogenetic Trees.” Bioinformatics (Oxford, England) 17 (8): 754–55.

Huson, Daniel H., and Celine Scornavacca. 2012. “Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks.” Systematic Biology 61 (6): 1061–7. https://doi.org/10.1093/sysbio/sys062.

Jombart, Thibaut, David M. Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, et al. 2014. “OutbreakTools: A New Platform for Disease Outbreak Analysis Using the R Software.” Epidemics 7 (June): 28–34. https://doi.org/10.1016/j.epidem.2014.04.003.

Kostic, Aleksandar D, Dirk Gevers, Chandra Sekhar Pedamallu, Monia Michaud, Fujiko Duke, Ashlee M Earl, Akinyemi I Ojesina, et al. 2012. “Genomic Analysis Identifies Association of Fusobacterium with Colorectal Carcinoma.” Genome Research 22 (2): 292–98. https://doi.org/10.1101/gr.126573.111.

Kuczynski, Justin, Jesse Stombaugh, William Anton Walters, Antonio González, J. Gregory Caporaso, and Rob Knight. 2011. “Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities.” Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [et Al.] CHAPTER (December): Unit10.7. https://doi.org/10.1002/0471250953.bi1007s36.

Kumar, Sudhir, Glen Stecher, and Koichiro Tamura. 2016. “MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.” Molecular Biology and Evolution 33 (7): 1870–4. https://doi.org/10.1093/molbev/msw054.

Kunin, Victor, and Philip Hugenholtz. 2010. “PyroTagger : A Fast , Accurate Pipeline for Analysis of rRNA Amplicon Pyrosequence Data.” The Open Journal, 1–8. http://www.theopenjournal.org/toj_articles/1.

Lam, Tommy Tsan-Yuk, Chung-Chau Hon, Philippe Lemey, Oliver G. Pybus, Mang Shi, Hein Min Tun, Jun Li, Jingwei Jiang, Edward C. Holmes, and Frederick Chi-Ching Leung. 2012. “Phylodynamics of H5N1 Avian Influenza Virus in Indonesia.” Molecular Ecology 21 (12): 3062–77. https://doi.org/10.1111/j.1365-294X.2012.05577.x.

Lam, Tommy Tsan-Yuk, Boping Zhou, Jia Wang, Yujuan Chai, Yongyi Shen, Xinchun Chen, Chi Ma, et al. 2015. “Dissemination, Divergence and Establishment of H7N9 Influenza Viruses in China.” Nature 522 (7554): 102–5. https://doi.org/10.1038/nature14348.

Larsen, Frederik T., Bertrand Bed’Hom, Bernt Guldbrandtsen, and Tina S. Dalgaard. 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 (October): 216–25. https://doi.org/10.1016/j.molimm.2019.07.022.

Lemmon, Alan R., and Emily C. Moriarty. 2004. “The Importance of Proper Model Assumption in Bayesian Phylogenetics.” Systematic Biology 53 (2): 265–77. https://doi.org/10.1080/10635150490423520.

Letunic, Ivica, and Peer Bork. 2007. “Interactive Tree of Life (iTOL): An Online Tool for Phylogenetic Tree Display and Annotation.” Bioinformatics 23 (1): 127–28. https://doi.org/10.1093/bioinformatics/btl529.

Liang, Huyi, Tommy Tsan-Yuk Lam, Xiaohui Fan, Xinchun Chen, Yu Zeng, Ji Zhou, Lian Duan, et al. 2014. “Expansion of Genotypic Diversity and Establishment of 2009 H1N1 Pandemic-Origin Internal Genes in Pigs in China.” Journal of Virology, July, JVI.01327–14. https://doi.org/10.1128/JVI.01327-14.

Lott, Steffen C., Björn Voß, Wolfgang R. Hess, and Claudia Steglich. 2015. “CoVennTree: A New Method for the Comparative Analysis of Large Datasets.” Frontiers in Genetics 6: 43. https://doi.org/10.3389/fgene.2015.00043.

Maddison, David R., David L. Swofford, Wayne P. Maddison, and David Cannatella. 1997. “Nexus: An Extensible File Format for Systematic Information.” Systematic Biology 46 (4): 590–621. https://doi.org/10.1093/sysbio/46.4.590.

Matsen, Frederick A., Noah G. Hoffman, Aaron Gallagher, and Alexandros Stamatakis. 2012. “A Format for Phylogenetic Placements.” PLoS ONE 7 (2): e31009. https://doi.org/10.1371/journal.pone.0031009.

Matsen, Frederick A., Robin B. Kodner, and E Virginia Armbrust. 2010. “Pplacer: Linear Time Maximum-Likelihood and Bayesian Phylogenetic Placement of Sequences onto a Fixed Reference Tree.” BMC Bioinformatics 11: 538. https://doi.org/10.1186/1471-2105-11-538.

Matsen, Frederick A, Robin B Kodner, and E Virginia Armbrust. 2010. “Pplacer: Linear Time Maximum-Likelihood and Bayesian Phylogenetic Placement of Sequences onto a Fixed Reference Tree.” BMC Bioinformatics 11 (1): 538. https://doi.org/10.1186/1471-2105-11-538.

McMurdie, Paul J., and Susan Holmes. 2013. “Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data.” PLoS ONE 8 (4): e61217. https://doi.org/10.1371/journal.pone.0061217.

Michonneau, François, Joseph W. Brown, and David J. Winter. 2016. “Rotl: An R Package to Interact with the Open Tree of Life Data.” Methods in Ecology and Evolution 7 (12): 1476–81. https://doi.org/10.1111/2041-210X.12593.

Morgan, Xochitl C., Nicola Segata, and Curtis Huttenhower. 2013. “Biodiversity and Functional Genomics in the Human Microbiome.” Trends in Genetics 29 (1): 51–58. https://doi.org/10.1016/J.TIG.2012.09.005.

Neher, Richard A., Trevor Bedford, Rodney S. Daniels, Colin A. Russell, and Boris I. Shraiman. 2016. “Prediction, Dynamics, and Visualization of Antigenic Phenotypes of Seasonal Influenza Viruses.” Proceedings of the National Academy of Sciences 113 (12): E1701–E1709. https://doi.org/10.1073/pnas.1525578113.

Page, Roderic D. M. 2002. “Visualizing Phylogenetic Trees Using TreeView.” Current Protocols in Bioinformatics Chapter 6 (August): Unit 6.2. https://doi.org/10.1002/0471250953.bi0602s01.

Paradis, Emmanuel, Julien Claude, and Korbinian Strimmer. 2004. “APE: Analyses of Phylogenetics and Evolution in R Language.” Bioinformatics 20 (2): 289–90. https://doi.org/10.1093/bioinformatics/btg412.

Pond, Sergei L. Kosakovsky, Simon D. W. Frost, and Spencer V. Muse. 2005. “HyPhy: Hypothesis Testing Using Phylogenies.” Bioinformatics (Oxford, England) 21 (5): 676–79. https://doi.org/10.1093/bioinformatics/bti079.

Rannala, B., and Z. Yang. 1996. “Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference.” Journal of Molecular Evolution 43 (3): 304–11.

R Core Team. 2016. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

Retief, J. D. 2000. “Phylogenetic Analysis Using PHYLIP.” Methods in Molecular Biology (Clifton, N.J.) 132: 243–58.

Revell, Liam J. 2012. “Phytools: An R Package for Phylogenetic Comparative Biology (and Other Things).” Methods in Ecology and Evolution 3 (2): 217–23. https://doi.org/10.1111/j.2041-210X.2011.00169.x.

Sanderson, Michael J. 2003. “R8s: Inferring Absolute Rates of Molecular Evolution and Divergence Times in the Absence of a Molecular Clock.” Bioinformatics 19 (2): 301–2. https://doi.org/10.1093/bioinformatics/19.2.301.

Schliep, Klaus Peter. 2011. “Phangorn: Phylogenetic Analysis in R.” Bioinformatics 27 (4): 592–93. https://doi.org/10.1093/bioinformatics/btq706.

Schloss, Patrick D., Sarah L. Westcott, Thomas Ryabin, Justine R. Hall, Martin Hartmann, Emily B. Hollister, Ryan A. Lesniewski, et al. 2009. “Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities.” Applied and Environmental Microbiology 75 (23): 7537–41. https://doi.org/10.1128/AEM.01541-09.

Schmidt, Heiko A., Korbinian Strimmer, Martin Vingron, and Arndt von Haeseler. 2002. “TREE-PUZZLE: Maximum Likelihood Phylogenetic Analysis Using Quartets and Parallel Computing.” Bioinformatics (Oxford, England) 18 (3): 502–4.

Schön, Isa, Rylan Shearn, Koen Martens, Annette Koenders, and Stuart Halse. 2015. “Age and Origin of Australian Bennelongia (Crustacea, Ostracoda).” Hydrobiologia 750 (1): 125–46. https://doi.org/10.1007/s10750-014-2159-z.

Segata, Nicola, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, and Curtis Huttenhower. 2011. “Metagenomic Biomarker Discovery and Explanation.” Genome Biology 12 (6): R60. https://doi.org/10.1186/gb-2011-12-6-r60.

Shoemaker, J. S., and W. M. Fitch. 1989. “Evidence from Nuclear Sequences That Invariable Sites Should Be Considered When Sequence Divergence Is Calculated.” Molecular Biology and Evolution 6 (3): 270–89.

Stamatakis, Alexandros. 2014. “RAxML Version 8: A Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.” Bioinformatics, January, btu033. https://doi.org/10.1093/bioinformatics/btu033.

Venkatesh, Divya, Marjolein J. Poen, Theo M. Bestebroer, Rachel D. Scheuer, Oanh Vuong, Mzia Chkhaidze, Anna Machablishvili, et al. 2018. “Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem.” Journal of Virology 92 (15). https://doi.org/10.1128/JVI.00433-18.

Vos, Rutger A., James P. Balhoff, Jason A. Caravas, Mark T. Holder, Hilmar Lapp, Wayne P. Maddison, Peter E. Midford, et al. 2012. “NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.” Systematic Biology 61 (4): 675–89. https://doi.org/10.1093/sysbio/sys025.

Wang, Li-Gen, Tommy Tsan-Yuk Lam, Shuangbin Xu, Zehan Dai, Lang Zhou, Tingze Feng, Pingfan Guo, et al. 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. https://doi.org/10.1093/molbev/msz240.

Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer. http://ggplot2.org.

Wilgenbusch, James C., and David Swofford. 2003. “Inferring Evolutionary Trees with PAUP*.” Current Protocols in Bioinformatics Chapter 6 (February): Unit 6.4. https://doi.org/10.1002/0471250953.bi0604s00.

Wilkinson, Leland, D. Wills, D. Rope, A. Norton, and R. Dubbs. 2005. The Grammar of Graphics. 2nd edition. New York: Springer.

Wong, Vanessa K., Stephen Baker, Derek J. Pickard, Julian Parkhill, Andrew J. Page, Nicholas A. Feasey, Robert A. Kingsley, et al. 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): 632–39. https://doi.org/10.1038/ng.3281.

Wu, Na, Xi Yang, Ruifen Zhang, Jun Li, Xue Xiao, Yongfei Hu, Yanfei Chen, et al. 2013. “Dysbiosis Signature of Fecal Microbiota in Colorectal Cancer Patients.” Microbial Ecology 66 (2): 462–70. https://doi.org/10.1007/s00248-013-0245-9.

Yang, Z. 1994. “Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods.” Journal of Molecular Evolution 39 (3): 306–14.

Yang, Ziheng. 2007. “PAML 4: Phylogenetic Analysis by Maximum Likelihood.” Molecular Biology and Evolution 24 (8): 1586–91. https://doi.org/10.1093/molbev/msm088.

Yu, Guangchuang. 2020. “Using Ggtree to Visualize Data on Tree-Like Structures.” Current Protocols in Bioinformatics 69 (1): e96. https://doi.org/10.1002/cpbi.96.

Yu, Guangchuang, Tommy Tsan-Yuk Lam, Huachen Zhu, and Yi Guan. 2018. “Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree.” Molecular Biology and Evolution 35 (12): 3041–3. https://doi.org/10.1093/molbev/msy194.

Yu, Guangchuang, David K. Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 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. https://doi.org/10.1111/2041-210X.12628.

Zmasek, Christian M., and Sean R. Eddy. 2001. “ATV: Display and Manipulation of Annotated Phylogenetic Trees.” Bioinformatics 17 (4): 383–84. https://doi.org/10.1093/bioinformatics/17.4.383.