ViCTree is a bioinformatics framework that automatically selects new candidate virus sequences from GenBank, generates multiple sequence alignments, calculates a maximum likelihood phylogeny and, is capable of automatically building new phylogenies when new data is available on GenBank.
For documentation please visit ViCTree website: http://bioinformatics.cvr.ac.uk/victree_web/
You can also find the documentation here.
An instance of the visualisation component of the framework called ViCTreeView is available at http://www.bioinformatics.cvr.ac.uk/ViCTree
ViCTreeView is developed by Anil Thanki.
Sejal Modha, Anil Thanki, Susan F Cotmore, Andrew J Davison, Joseph Hughes; ViCTree: An automated framework for taxonomic classification from protein sequences, Bioinformatics, bty099, https://doi.org/10.1093/bioinformatics/bty099
Please submit any questions or inquires to GitHub issues page: https://github.com/josephhughes/ViCTree/issues
If you use ViCTree please cite following tools.
1. BLAST
Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–10
2. CD-HIT
Fu,L. et al. (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150–3152.
3. Clustal Omega
Sievers,F. et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol., 7, 539.
4. mPTP
Kapli,P. et al. (2017) Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics, 33, 1630–1638.
5. RAxML
Stamatakis,A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313.