References
Gonzalez, A. et al. Qiita: rapid, web-enabled microbiome meta-analysis. Nat. Methods 15, 796–798 (2018).
Zhu, Q. et al. Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy. mSystems 7, e00167-22 (2022).
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
Zhu, Q. et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat. Commun. 10, 5477 (2019).
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38, 1079–1086 (2020).
Mirarab, S., Nakhleh, L. & Warnow, T. Multispecies coalescent: theory and applications in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 52, 247–268 (2021).
Davidson, R., Vachaspati, P., Mirarab, S. & Warnow, T. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics 16, S1 (2015).
Maddison, W. P. Gene trees in species trees. Syst. Biol. 46, 523–536 (1997).
Degnan, J. H. & Rosenberg, N. A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24, 332–340 (2009).
Gogarten, J. P., Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226–2238 (2002).
Creevey, C. J., Doerks, T., Fitzpatrick, D. A., Raes, J. & Bork, P. Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS ONE 6, e22099 (2011).
Yan, Z., Smith, M. L., Du, P., Hahn, M. W. & Nakhleh, L. Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs. Syst. Biol. 71, 367–381 (2022).
Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 11, 2500 (2020).
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
Mirarab, S. et al. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541–i548 (2014).
Matsen, F. A., Kodner, R. B. & Armbrust, E. V. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11, 538 (2010).
Rabiee, M. & Mirarab, S. INSTRAL: discordance-aware phylogenetic placement using quartet scores. Syst. Biol. 69, 384–391 (2020).
Wedell, E., Cai, Y. & Warnow, T. SCAMPP: scaling alignment-based phylogenetic placement to large trees. IEEE/ACM Trans. Comput. Biol. Bioinform. 20, 1417–1430 (2023).
Barbera, P. et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol. 68, 365–369 (2019).
Warnow, T. (ed.) Bioinformatics and Phylogenetics 121–150 (Springer, 2019).
Nelesen, S. M., Liu, K., Wang, L.-S., Linder, C. R. & Warnow, T. DACTAL: divide-and-conquer trees (almost) without alignments. Bioinformatics 28, i274–i282 (2012).
Huson, D. H., Nettles, S. M. & Warnow, T. J. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6, 369–386 (1999).
Balaban, M. et al. Generation of accurate, expandable phylogenomic trees with uDance. GitHub https://github.com/balabanmetin/uDance (2023).
Balaban, M., Jiang, Y., Roush, D., Zhu, Q. & Mirarab, S. Fast and accurate distance-based phylogenetic placement using divide and conquer. Mol. Ecol. Resour. 22, 1213–1227 (2022).
Rabiee, M. & Mirarab, S. Forcing external constraints on tree inference using ASTRAL. BMC Genomics 21, 218 (2020).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree-2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Yin, J., Zhang, C. & Mirarab, S. ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics 35, 3961–3969 (2019).
Vachaspati, P. & Warnow, T. ASTRID: accurate species TRees from internode distances. BMC Genomics 16, S3 (2015).
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618 (2012).
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
Coleman, G. A. et al. A rooted phylogeny resolves early bacterial evolution. Science 372, eabe0511 (2021).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).
Sayyari, E. & Mirarab, S. Fast coalescent-based computation of local branch support from quartet frequencies. Mol. Biol. Evol. 33, 1654–1668 (2016).
Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019).
Jiang, Y., Balaban, M., Zhu, Q. & Mirarab, S. DEPP: deep learning enables extending species trees using single genes. Syst. Biol. 72, 17–34 (2023).
Jiang, Y., Tabaghi, P. & Mirarab, S. Learning hyperbolic embedding for phylogenetic tree placement and updates. Biology 11, 1256 (2022).
Nasko, D. J., Koren, S., Phillippy, A. M. & Treangen, T. J. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biol. 19, 165 (2018).
Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. Proc. Natl Acad. Sci. USA 113, 5970–5975 (2016).
Fullam A. et al. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res. 51, D760–D766 (2023).
Jukes, T. H. & Cantor, C. R. in Mammalian Protein Metabolism Vol. 3 (ed. Munro, H. N.) 21–132 (Academic Press, 1969).
Sonnhammer, E. L. L. & Hollich, V. Scoredist: a simple and robust protein sequence distance estimator. BMC Bioinformatics 6, 108 (2005).
Darriba, D. et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37, 291–294 (2020).
Anisimova, M., Gil, M., Dufayard, J.-F., Dessimoz, C. & Gascuel, O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst. Biol. 60, 685–699 (2011).
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Zhang, C., Zhao, Y., Braun, E. L. & Mirarab, S. TAPER: pinpointing errors in multiple sequence alignments despite varying rates of evolution. Methods Ecol. Evol. 12, 2145–2158 (2021).
Sayyari, E., Whitfield, J. B. & Mirarab, S. Fragmentary gene sequences negatively impact gene tree and species tree reconstruction. Mol. Biol. Evol. 34, 3279–3291 (2017).
Mai, U. & Mirarab, S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics 19, 272 (2018).
Balaban, M., Moshiri, N., Mai, U., Jia, X. & Mirarab, S. TreeCluster: clustering biological sequences using phylogenetic trees. PLoS ONE 14, e0221068 (2019).
Mölder, F. et al. Sustainable data analysis with Snakemake. F1000Res. 10, 33 (2021).
Mallo, D., De Oliveira Martins, L. & Posada, D. SimPhy: phylogenomic simulation of gene, locus, and species trees. Syst. Biol. 65, 334–344 (2016).
Fletcher, W. & Yang, Z. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26, 1879–1888 (2009).
Nguyen, N. D., Mirarab, S., Kumar, K. & Warnow, T. Ultra-large alignments using phylogeny-aware profiles. Genome Biol. 16, 124 (2015).
Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A.-M. K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431–449 (2000).
Haft, D. H. et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 46, D851–D860 (2018).
Segata, N., Börnigen, D., Morgan, X. C. & Huttenhower, C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun. 4, 2304 (2013).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2, e243 (2014).
Orakov, A. et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 22, 178 (2021).
Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
Wickett, N. J. et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl Acad. Sci. USA 111, 4859–4868 (2014).
Balaban, M. et al. Data for article: generation of accurate, expandable phylogenomic trees with uDance. Harvard Dataverse https://doi.org/10.7910/DVN/BCUM6P (2023).
Balaban, M. et al. Postprocessing data for article: generation of accurate, expandable phylogenomic trees with uDance. Zenodo https://doi.org/10.5281/zenodo.8057941 (2023).
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