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Cited by 73Genomics and Phylogenetic StudiesFractal and DNA sequence analysisRNA and protein synthesis mechanisms

DendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments

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Kelly, Steven, Maini, Philip K.·2013·PLoS ONE
DOI 10.1371/journal.pone.0058537PMC PMC3598851
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Abstract

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

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  • The accuracy of key component algorithms of OrthoFinder has been independently assessed in this work and in dedicated publications.

    “The accuracy of key component algorithms of OrthoFinder has been independently assessed in this work and in dedicated publications [5, 10, 22, 24, 33].”

    From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [24]

  • In benchmark tests, STAG had higher accuracy than other leading methods for species tree inference, including maximum likelihood species tree inference from concatenated alignments of protein sequences, ASTRAL and NJst.

    “In benchmark tests, STAG [24] had higher accuracy than other leading methods for species tree inference, including maximum likelihood species tree inference from concatenated alignments of protein sequences, ASTRAL [38] and NJst [39].”

    From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [24]

    The Methods and Results passages benchmark DendroBLAST, not STAG. Searches for STAG, ASTRAL, NJst, and the claimed comparison with concatenated protein alignments found no passage in this paper that evaluates STAG's accuracy against those methods. (LLM, conf=0.78)

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Research works printed but not linked: 40

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Cited by

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Authors
Kelly, S., & Maini, P. K.
Affiliations
University of Oxford (GB)
Corresponding author
Kelly, Steven
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2013-03-15
Volume
8
Issue
3
Pages
e58537
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0058537
PMC
PMC3598851
OpenAlex
W2074432684
Cited by
73
References
0
Citations by year
2026: 11 · 2025: 10 · 2024: 12 · 2023: 8 · 2022: 10 · 2021: 11 · 2020: 3 · 2019: 2 · 2018: 3 · 2016: 1 · 2015: 2
FWCI
0.38
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (acceptedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, cc-by)
Funders
  • Directorate for Biological Sciences
  • Biotechnology and Biological Sciences Research Council (BB/D020190/1)
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 › RNA and protein synthesis mechanisms
Keywords
phylogenetic inference, BLAST, protein sequences, genome-scale phylogenomics, web application
MeSH terms
Algorithms, Archaea, Phylogeny, Software, Sequence Alignment, Evolution, Molecular, Archaeal Proteins, Internet, Sequence Analysis, Protein

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