Generation of accurate, expandable phylogenomic trees with uDance

References

  1. Gonzalez, A. et al. Qiita: rapid, web-enabled microbiome meta-analysis. Nat. Methods 15, 796–798 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  2. Zhu, Q. et al. Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy. mSystems 7, e00167-22 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  3. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  4. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  5. 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  6. Zhu, Q. et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat. Commun. 10, 5477 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  7. Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38, 1079–1086 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  8. Mirarab, S., Nakhleh, L. & Warnow, T. Multispecies coalescent: theory and applications in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 52, 247–268 (2021).

    Article 

    Google Scholar
     

  9. 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  10. Maddison, W. P. Gene trees in species trees. Syst. Biol. 46, 523–536 (1997).

    Article 

    Google Scholar
     

  11. Degnan, J. H. & Rosenberg, N. A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24, 332–340 (2009).

    Article 
    PubMed 

    Google Scholar
     

  12. Gogarten, J. P., Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226–2238 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  13. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  14. 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).

    Article 
    PubMed 

    Google Scholar
     

  15. Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 11, 2500 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  16. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  17. Mirarab, S. et al. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541–i548 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  18. 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  19. Rabiee, M. & Mirarab, S. INSTRAL: discordance-aware phylogenetic placement using quartet scores. Syst. Biol. 69, 384–391 (2020).

  20. 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).

    Article 
    PubMed 

    Google Scholar
     

  21. Barbera, P. et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol. 68, 365–369 (2019).

    Article 
    PubMed 

    Google Scholar
     

  22. Warnow, T. (ed.) Bioinformatics and Phylogenetics 121–150 (Springer, 2019).

  23. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  24. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  25. Balaban, M. et al. Generation of accurate, expandable phylogenomic trees with uDance. GitHub https://github.com/balabanmetin/uDance (2023).

  26. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  27. Rabiee, M. & Mirarab, S. Forcing external constraints on tree inference using ASTRAL. BMC Genomics 21, 218 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  28. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree-2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

  29. Yin, J., Zhang, C. & Mirarab, S. ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics 35, 3961–3969 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  30. Vachaspati, P. & Warnow, T. ASTRID: accurate species TRees from internode distances. BMC Genomics 16, S3 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  31. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  32. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  33. Coleman, G. A. et al. A rooted phylogeny resolves early bacterial evolution. Science 372, eabe0511 (2021).

  34. Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  35. Sayyari, E. & Mirarab, S. Fast coalescent-based computation of local branch support from quartet frequencies. Mol. Biol. Evol. 33, 1654–1668 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  36. Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019).

  37. Jiang, Y., Balaban, M., Zhu, Q. & Mirarab, S. DEPP: deep learning enables extending species trees using single genes. Syst. Biol. 72, 17–34 (2023).

    Article 
    PubMed 

    Google Scholar
     

  38. Jiang, Y., Tabaghi, P. & Mirarab, S. Learning hyperbolic embedding for phylogenetic tree placement and updates. Biology 11, 1256 (2022).

  39. 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  40. Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. Proc. Natl Acad. Sci. USA 113, 5970–5975 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  41. Fullam A. et al. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res. 51, D760–D766 (2023).

  42. Jukes, T. H. & Cantor, C. R. in Mammalian Protein Metabolism Vol. 3 (ed. Munro, H. N.) 21–132 (Academic Press, 1969).

  43. Sonnhammer, E. L. L. & Hollich, V. Scoredist: a simple and robust protein sequence distance estimator. BMC Bioinformatics 6, 108 (2005).

  44. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  45. 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  46. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  47. 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).

    Article 

    Google Scholar
     

  48. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  49. Mai, U. & Mirarab, S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics 19, 272 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  50. Balaban, M., Moshiri, N., Mai, U., Jia, X. & Mirarab, S. TreeCluster: clustering biological sequences using phylogenetic trees. PLoS ONE 14, e0221068 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  51. Mölder, F. et al. Sustainable data analysis with Snakemake. F1000Res. 10, 33 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  52. Mallo, D., De Oliveira Martins, L. & Posada, D. SimPhy: phylogenomic simulation of gene, locus, and species trees. Syst. Biol. 65, 334–344 (2016).

    Article 
    PubMed 

    Google Scholar
     

  53. Fletcher, W. & Yang, Z. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26, 1879–1888 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  54. Nguyen, N. D., Mirarab, S., Kumar, K. & Warnow, T. Ultra-large alignments using phylogeny-aware profiles. Genome Biol. 16, 124 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  55. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  56. Haft, D. H. et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res. 46, D851–D860 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  57. 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).

    Article 
    PubMed 

    Google Scholar
     

  58. Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  59. Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2, e243 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  60. Orakov, A. et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 22, 178 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  61. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  62. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  63. 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).

    Article 

    Google Scholar
     

  64. 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).

  65. 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).

Download references

Note: This article have been indexed to our site. We do not claim legitimacy, ownership or copyright of any of the content above. To see the article at original source Click Here

Related Posts
Trace Gas Orbiter Spots ‘Tree Stump’ Crater on Mars thumbnail

Trace Gas Orbiter Spots ‘Tree Stump’ Crater on Mars

ESA’s Trace Gas Orbiter (TGO) has spotted an ice-rich impact crater in Acidalia Planitia, a Martian plain between the Tharsis volcanic province and Arabia Terra to the north of Valles Marineris. This image from ESA’s Trace Gas Orbiter shows a giant impact crater in Acidalia Planitia on Mars. Image credit: ESA / CaSSIS / CC…
Read More

Publisher Correction: Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast

Correction to: Nature Biotechnology https://doi.org/10.1038/s41587-021-00959-8, published online 8 July 2021.In the version of this Article initially published, there was an error in Fig. 3. Specifically, in Fig. 3a, the lower blue equation at left, the denominator in the final term was a duplication of the second-to-last term, mistakenly reading “koff + kclv” when it should…
Read More
How to Delete Your Discord Account thumbnail

How to Delete Your Discord Account

If you’re no longer an active Discord user, and you don’t think you’ll be returning to the service anytime soon, it’s a good idea to delete your Discord account. The service makes it easy to do that, and we’ll show you how. RELATED: 8 Ways to Personalize Your Discord Account What to Know Before Deleting…
Read More
How to Make a Cheap DIY Canopy Bed thumbnail

How to Make a Cheap DIY Canopy Bed

Photo: Archi_Viz (Shutterstock)Canopy beds can make your bedroom feel romantic, calm, and peaceful. But canopy beds themselves are, well, expensive. You can get the canopy look, though, but without the cost. Just make your own.What you’ll need for your canopy bedFor these projects, you’ll need a tape measure, screw gun, and a stud finder. And…
Read More
Index Of News