ViPTree : the Viral Proteomic Tree server

About

ViPTree helps to generate a "proteomic tree" of viral genome sequences based on genome-wide sequence similarities computed by tBLASTx. The original proteomic tree concept (i.e., "the Phage Proteomic Tree”) was developed by Rohwer and Edwards, 2002. A proteomic tree is a dendrogram that reveals global genomic similarity relationships between tens, hundreds, or thousands of viruses. It has been shown that viral groups identified in a proteomic tree well correspond to established viral taxonomies. The proteomic tree approach is effective to investigate genomes of newly sequenced viruses as well as those identified in metagenomes.

Workflow

Browse trees of reference viral genomes

  1. Select nucleic acid types: dsDNA / ssDNA / dsRNA / ssRNA viruses, retroviruses, satellite viruses and virophages
  2. Select host categories: prokaryotic / eukaryotic / any host
  3. Browse proteomic trees and alignments between reference viruses
  4. Download figures and tables

Generate a proteomic tree of your viruses

  1. Upload your viral sequences and choose reference viruses to generate a proteomic tree
  2. Browse the generated proteomic tree
  3. Regenerate a new smaller proteomic tree only with viruses selected from the previously generated entire proteomic tree to enhance the investigation of your viruses
  4. Browse dotplots / genomic alignments between your viruses and reference viruses
  5. Browse genomic similarity scores and gene annotation
  6. Download figures and tables

Snapshots

Documentation

Further features and instructions are written in the documentation page.

Code availability

Source code for viral proteomic tree generation is available.
Download ViPTreeGen (standalone version)

Reference virus data download

Reference viral sequences and taxonomic information are downloadable from Virus-Host DB.

Related work

We performed a marine EVG (environmental viral genome) study by using a prototype of the ViPTree server.
Supplemental data is available.

Citation

If you use results (data / figures) genereted by ViPTree in your research, please cite:
  • Nishimura, Y. et al. ViPTree: the viral proteomic tree server. (submitted)

Following papers are related in methodological aspects to the ViPTree server.
  • Nishimura, Y. et al. Environmental viral genomes shed new light on virus–host interactions in the ocean.
  • mSphere (accepted)
  • Bhunchoth, Y. et al. Two asian jumbo phages, ϕRSL2 and ϕRSF1, infect Ralstonia solanacearum and show common features of ϕKZ-related phages.
  • Virology 494, 56-66, doi:10.1016/j.virol.2016.03.028, (2016).

Feedback

We appreciate bug reports, comments, and suggestions. The form is here.