ViCTree: an automated framework for taxonomic classification from protein sequences

The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualization tool that enables the tree to be explored interactively in the context of pairwise distance data. To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/. Supplementary data are available at Bioinformatics online.

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Author Modha, Sejal
Last Updated November 20, 2019, 16:47 (UTC)
Created August 1, 2019, 10:29 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type implied-oa
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1093/bioinformatics/bty099
DOI 10.1093/bioinformatics/bty099
Date Last Updated 2019-04-02T18:28:03.300558
Evidence open (via page says Open Access)
Funder code(s) Medical Research Council (MC_UU_12014/12)
Journal Is Open Access false
Open Access Status hybrid
PDF URL https://academic.oup.com/bioinformatics/article-pdf/34/13/2195/25098127/bty099.pdf
Publisher URL https://doi.org/10.1093/bioinformatics/bty099