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Cited by 67Genomics and Phylogenetic StudiesFractal and DNA sequence analysisBioinformatics and Genomic Networks

SHOOT: phylogenetic gene search and ortholog inference

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Emms, David Mark, Kelly, Steven·2022·Genome Biology
DOI 10.1186/s13059-022-02652-8PMC PMC8962542

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Abstract

Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this analysis with comparable speed to a BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional tree inference, and it can identify orthologs with high accuracy. In summary, SHOOT is a fast and accurate tool for phylogenetic analyses of novel query sequences. It is available online at www.shoot.bio .

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  • The SHOOT profile algorithm enables rapid addition of new species to existing OrthoFinder runs.

    “This is achieved through adaptation and further development of the SHOOT profile algorithm19, which enables rapid addition of new species to existing OrthoFinder runs.”

    From OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability (2026) · cites this paper as [19]

    The Materials and methods sections on database preparation and search describe SHOOT profiles assigning novel gene sequences to precomputed trees for rapid phylogenetic placement. They do not say that the algorithm adds new species to existing OrthoFinder runs; OrthoFinder results are instead described as input to SHOOT database preparation. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • It is possible to rapidly and accurately place individual sequences into a database of phylogenetic trees and biological sequences produced by an OrthoFinder search.

    “In recent work, we showed that it was possible to rapidly and accurately place individual sequences into a database of phylogenetic trees and biological sequences produced by an OrthoFinder search19.”

    From OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability (2026) · cites this paper as [19]

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Research works printed but not linked: 36

  1. [1]Needleman SB Wunsch CD A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 1970 48 443 453 10.1016/0022-2836(70)90057-4 5420325 · DOI · Paper page
  2. [2]Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981 147 195 197 10.1016/0022-2836(81)90087-5 7265238 · DOI
  3. [3]Lipman DJ Pearson WR Rapid and sensitive protein similarity searches Science 1985 227 1435 1441 10.1126/science.2983426 2983426 · DOI · Paper page
  4. [4]Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990 215 403 410 10.1016/S0022-2836(05)80360-2 2231712 · DOI · Paper page
  5. [5]Edgar RC Search and clustering orders of magnitude faster than BLAST Bioinformatics 2010 26 2460 2461 10.1093/bioinformatics/btq461 20709691 · DOI
  6. [6]Buchfink B Xie C Huson DH Fast and sensitive protein alignment using DIAMOND Nat Methods 2015 12 59 60 10.1038/nmeth.3176 25402007 · DOI · Paper page
  7. [7]Hauser M Steinegger M Soding J MMseqs software suite for fast and deep clustering and searching of large protein sequence sets Bioinformatics 2016 32 1323 1330 10.1093/bioinformatics/btw006 26743509 · DOI
  8. [8]Schreiber F Patricio M Muffato M Pignatelli M Bateman A TreeFam v9: a new website, more species and orthology-on-the-fly Nucleic Acids Res 2014 42 D922 D925 10.1093/nar/gkt1055 24194607 PMC3965059 · DOI
  9. [9]Tang H Finn RD Thomas PD TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations Bioinformatics 2019 35 518 520 10.1093/bioinformatics/bty625 30032202 PMC6361231 · DOI
  10. [10]Cantalapiedra CP Hernandez-Plaza A Letunic I Bork P Huerta-Cepas J eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale Mol Biol Evol 2021 38 5825 5829 10.1093/molbev/msab293 34597405 PMC8662613 · DOI
  11. [11]Bucchini F, Del Cortona A, Kreft L, Botzki A, Van Bel M, Vandepoele K. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. Nucleic Acids Res. 2021;49(17):e101. 10.1093/nar/gkab565. PMC8464036 34197621 · DOI
  12. [12]Kelly S, Maini PK. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments. PLoS One. 2013;8(3):e58537. 10.1371/journal.pone.0058537. PMC3598851 23554899 · DOI · Paper page
  13. [13]Camacho C Coulouris G Avagyan V Ma N Papadopoulos J Bealer K Madden TL BLAST+: architecture and applications BMC Bioinformatics 2009 10 421 10.1186/1471-2105-10-421 20003500 PMC2803857 · DOI · Paper page
  14. [14]Mirdita M Steinegger M Soding J MMseqs2 desktop and local web server app for fast, interactive sequence searches Bioinformatics 2019 35 2856 2858 10.1093/bioinformatics/bty1057 30615063 PMC6691333 · DOI · Paper page
  15. [15]Barbera P Kozlov AM Czech L Morel B Darriba D Flouri T Stamatakis A EPA-ng: massively parallel evolutionary placement of genetic sequences Syst Biol 2019 68 365 369 10.1093/sysbio/syy054 30165689 PMC6368480 · DOI
  16. [17]Buchfink B Reuter K Drost HG Sensitive protein alignments at tree-of-life scale using DIAMOND Nat Methods 2021 18 366 368 10.1038/s41592-021-01101-x 33828273 PMC8026399 · DOI · Paper page
  17. [18]Manning CD Raghavan P Schütze H Introduction to information retrieval 2008 New York Cambridge University Press
  18. [19]Huerta-Cepas J Bueno A Dopazo JQ Gabaldon T PhylomeDB: a database for genome-wide collections of gene phylogenies Nucleic Acids Res 2008 36 D491 D496 10.1093/nar/gkm899 17962297 PMC2238872 · DOI
  19. [20]Mi H Dong Q Muruganujan A Gaudet P Lewis S Thomas PD PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium Nucleic Acids Res 2010 38 D204 D210 10.1093/nar/gkp1019 20015972 PMC2808919 · DOI
  20. [21]Altenhoff AM Garrayo-Ventas J Cosentino S Emms D Glover NM Hernandez-Plaza A Nevers Y Sundesha V Szklarczyk D Fernandez JM The quest for orthologs benchmark service and consensus calls in 2020 Nucleic Acids Res 2020 48 W538 W545 10.1093/nar/gkaa308 32374845 PMC7319555 · DOI
  21. [22]Steinegger M Soding J MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Nat Biotechnol 2017 35 1026 1028 10.1038/nbt.3988 29035372 · DOI · Paper page
  22. [23]Dalquen DA Dessimoz C Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals Genome Biol Evol 2013 5 1800 1806 10.1093/gbe/evt132 24013106 PMC3814191 · DOI · Paper page
  23. [25]Emms DM Kelly S Benchmarking orthogroup inference accuracy: revisiting orthobench Genome Biol Evol 2020 12 2258 2266 10.1093/gbe/evaa211 33022036 PMC7738749 · DOI · Paper page
  24. [26]Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157. 10.1186/s13059-015-0721-2. PMC4531804 26243257 · DOI · Paper page
  25. [27]Nakamura T Yamada KD Tomii K Katoh K Parallelization of MAFFT for large-scale multiple sequence alignments Bioinformatics 2018 34 2490 2492 10.1093/bioinformatics/bty121 29506019 PMC6041967 · DOI
  26. [28]Minh BQ Schmidt HA Chernomor O Schrempf D Woodhams MD von Haeseler A Lanfear R IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era Mol Biol Evol 2020 37 1530 1534 10.1093/molbev/msaa015 32011700 PMC7182206 · DOI · Paper page
  27. [30]Czech L Barbera P Stamatakis A Methods for automatic reference trees and multilevel phylogenetic placement Bioinformatics 2019 35 1151 1158 10.1093/bioinformatics/bty767 30169747 PMC6449752 · DOI
  28. [31]Huerta-Cepas J Serra F Bork P ETE 3: reconstruction, analysis, and visualization of phylogenomic data Mol Biol Evol 2016 33 1635 1638 10.1093/molbev/msw046 26921390 PMC4868116 · DOI
  29. [32]Goodstein DM Shu SQ Howson R Neupane R Hayes RD Fazo J Mitros T Dirks W Hellsten U Putnam N Rokhsar DS Phytozome: a comparative platform for green plant genomics Nucleic Acids Res 2012 40 D1178 D1186 10.1093/nar/gkr944 22110026 PMC3245001 · DOI
  30. [33]Howe KL Achuthan P Allen J Allen J Alvarez-Jarreta J Amode MR Armean IM Azov AG Bennett R Bhai J Ensembl 2021 Nucleic Acids Res 2021 49 D884 D891 10.1093/nar/gkaa942 33137190 PMC7778975 · DOI
  31. [34]UniProt C UniProt: the universal protein knowledgebase in 2021 Nucleic Acids Res 2021 49 D480 D489 10.1093/nar/gkaa1100 33237286 PMC7778908 · DOI · Paper page
  32. [35]Tange O GNU Parallel - the command-line power tool login: The USENIX Magazine 2011 36 42 47
  33. [36]Stamatakis A RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 2014 30 1312 1313 10.1093/bioinformatics/btu033 24451623 PMC3998144 · DOI · Paper page
  34. [37]Shank SD, Weaver S, Kosakovsky Pond SL. phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics. 2018;19(1):276. 10.1186/s12859-018-2283-2. PMC6060545 30045713 · DOI
  35. [38]Emms D, Kelly S. SHOOT: phylogenetic gene search and ortholog inference. GitHub. 2021; https://github.com/davidemms/SHOOT. PMC8962542 35346327
  36. [39]Emms D, Kelly S. Dataset for, “SHOOT: phylogenetic gene search and ortholog inference”. 2021. 10.5281/zenodo.5602736. PMC8962542 35346327 · DOI

Cited by

Sorted by citations

Authors
Emms, D. M., & Kelly, S.
Affiliations
University of Oxford (GB)
Corresponding author
  • Emms, David Mark
  • Kelly, Steven
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2022-03-28
Volume
23
Issue
1
Pages
85-85
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-022-02652-8
PMC
PMC8962542
OpenAlex
W4220713476
Cited by
67
References
2
Citations by year
2026: 12 · 2025: 13 · 2024: 21 · 2023: 12 · 2022: 8 · 2021: 1
FWCI
4.89
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by)
Funders
  • Horizon 2020 Framework Programme (637765)
  • Royal Society
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
phylogenetic placement, gene phylogeny, phylogenetic tree, comparative genomics, BLAST comparison
MeSH terms
Algorithms, Biological Evolution, Phylogeny

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