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Bioinformatics. 2019 Jan 1;35(1):149-151. doi: 10.1093/bioinformatics/bty631.

SonicParanoid: fast, accurate and easy orthology inference.

Author information

1
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
2
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
3
Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.

Abstract

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.

PMID:
30032301
PMCID:
PMC6298048
DOI:
10.1093/bioinformatics/bty631
[Indexed for MEDLINE]
Free PMC Article

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