SonicParanoid: fast, accurate and easy orthology inference
Open accessAbstract
Motivation: Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ. Results: Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets. Availability and implementation: SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid. Supplementary information: Supplementary data are available at Bioinformatics online.
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Heuristic analysis of pairwise sequence similarity scores is based on the premise that higher scoring sequence pairs are likely to have diverged more recently than lower scoring sequence pairs.
“The central premise underlying their use is that higher scoring sequence pairs are likely to have diverged more recently than lower scoring sequence pairs.”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [12]
The Materials and methods section describes SonicParanoid’s sequence-scoring function and alignment thresholds, but does not say that higher-scoring pairs diverged more recently. Searches for the quoted premise and for a relationship between similarity scores and divergence time found no passage addressing that relationship; no page numbers are available in our copy. (LLM, conf=0.72)
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Research works printed but not linked: 18
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OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676 · see citing works
Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d
- Authors
- Cosentino, S., & Iwasaki, W.
- Affiliations
- The University of Tokyo (JP)
- Atmosphere and Ocean Research Institute, The University of Tokyo (JP)
- Corresponding author
- Cosentino, Salvatore
- Iwasaki, Wataru
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-07-19
- Volume
- 35
- Issue
- 1
- Pages
- 149-151
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6298048
- OpenAlex
- W2882992890
- Cited by
- 134
- References
- 0
- Citations by year
- 2026: 9 · 2025: 15 · 2024: 25 · 2023: 21 · 2022: 27 · 2021: 16 · 2020: 17 · 2019: 4
- FWCI
- 3.23
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Japanese Society for the Promotion of Scienc (16H06154, 16H06279, 17H05834)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- orthology inference, genome annotation, precision-recall trade-off, comparative genomics, Python
- MeSH terms
- Software, Genome, Computational Biology, Genomics, Databases, Genetic
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