Modha, S. , Thanki, A., Cotmore, S. F., Davison, A. J. and Hughes, J. (2018) ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics, 34(13), pp. 2195-2200. (doi: 10.1093/bioinformatics/bty099) (PMID:29474519) (PMCID:PMC6022645)
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Abstract
Motivation: 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 visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: 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/.
Item Type: | Articles |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Hughes, Dr Joseph and Davison, Professor Andrew and Modha, Ms Sejal |
Authors: | Modha, S., Thanki, A., Cotmore, S. F., Davison, A. J., and Hughes, J. |
College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
Journal Name: | Bioinformatics |
Publisher: | Oxford University Press |
ISSN: | 1367-4803 |
ISSN (Online): | 1460-2059 |
Published Online: | 20 February 2018 |
Copyright Holders: | Copyright © 2018 The Authors |
First Published: | First published in Bioinformatics 34(13): 2195-2200 |
Publisher Policy: | Reproduced under a Creative Commons License |
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