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SonicParanoid: fast, accurate and easy orthology inference

Salvatore Cosentino¹, Wataru Iwasaki^1,2,3

¹Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Bioinformatics (Oxford, England)

|July 23, 2018

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.

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