SonicParanoid: fast, accurate and easy orthology inference

Bioinformatics
Salvatore Cosentino, Wataru Iwasaki

Abstract

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. 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. 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 data are available at Bioinformatics online.

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Citations

Apr 7, 2020·International Journal of Systematic and Evolutionary Microbiology·Yasuhiro TanizawaMasanori Tohno
Jul 14, 2020·Bioinformatics·Dina SvetlitskyMichal Ziv-Ukelson
Jul 1, 2020·Molecular Biology and Evolution·Romain DerelleJohn K Colbourne
Sep 17, 2020·Briefings in Bioinformatics·Eva S DeutekomTeunis J P van Dam
Oct 28, 2019·GigaScience·Xiao Hu, Iddo Friedberg
Nov 16, 2019·Genome Biology·David M Emms, Steven Kelly
Sep 5, 2020·Molecular Biology and Evolution·Connor D HarrisLouis-Marie Bobay
Oct 6, 2020·FEMS Microbiology Ecology·Masaru BambaTakashi Tsuchimatsu
Oct 7, 2020·Genome Biology and Evolution·David M Emms, Steven Kelly
Jan 6, 2021·Nature Biotechnology·Jakob Nybo NissenSimon Rasmussen
Apr 7, 2021·Molecular Biology and Evolution·Benjamin LinardUNKNOWN QFO Consortium
Jul 16, 2021·International Journal of Systematic and Evolutionary Microbiology·Masanori TohnoHisami Kobayashi
Aug 14, 2021·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideaki YuasaTakehiko Itoh
Nov 9, 2021·International Journal of Systematic and Evolutionary Microbiology·Hisami KobayashiMasanori Tohno
Dec 17, 2021·International Journal of Systematic and Evolutionary Microbiology·Masanori TohnoHisami Kobayashi
Jan 6, 2022·Microbiology Spectrum·Jiro F Mori, Robert A Kanaly
Jan 13, 2022·Genome Biology and Evolution·Zoe VanceAoife McLysaght

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Software Mentioned

Proteinortho
BLASTP
MultiParanoid
OrthoMCL
SonicParanoid
PANTHER
legacy
OMA
OrthoFinder2
InParanoid

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