About

The ViPTree server generates 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, and 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. VipTree also offers an excellent alignment visualization useful for comparative genomics of viruses. You may also try DiGAlign, which extends VipTree's alignment visualization features that can be used for all nucleotide sequences, including non-viral genomes.

Workflow

Browse trees of reference viral genomes

Select nucleic acid types: dsDNA / dsDNA-RT / ssDNA / dsRNA / ssRNA / ssRNA-RT
Select host categories: prokaryotic / eukaryotic / any host
Browse proteomic trees and genomic alignments between reference viruses
Download figures and tables

Generate a proteomic tree of your viruses

Upload your viral sequences and choose reference viruses to generate a proteomic tree
Browse the proteomic tree
Regenerate a focused proteomic tree only with viruses selected from the entire proteomic tree for interpretation / presentation
Browse dotplots / genomic alignments between your viruses and reference viruses
Browse genomic similarity scores and gene annotation
Download figures and tables

Genome sequences and host information of reference viruses are based on the Virus-Host DB (Mihara et al., 2016).
Further information and instructions are available in the document page.

Example

Here is an exmaple of the session main page (an entrance page after the computation).

Snapshots

Circular proteomic tree: trees of prokaryotic dsDNA viruses (left) and eukaryotic ssDNA viruses (right), colored by virus families and host taxonomic groups.
Rectangular proteomic tree: a part of a dsDNA viruses tree, shown with virus names. Each of the inner nodes links to a genomic alignment of genomes that are included in its subtree.
Genomic alignmnet of metagenomic genome and Synechococcus phage S-SSM4.

Version history

2023-11-17 version 4.0

Major update! Various functions are newly implemented, as listed below.
Gene prediction is now performed by Prodigal and any coding table is selectable if it is compatible with Prodigal.
In the alignment viewer, threshold for tBLASTx/BLASTn could be set.
In the alignment viewer, a mouseover popup is implemented that shows details of genes and tBLASTx/BLASTn hits.
From this version, License is set as 'CC BY-NC-SA 4.0'
Many bug fixes, including the gene table upload function.
Document is updated.
Version of Virus-Host DB: RefSeq release 220

2023-08-11 version 3.7

Version of Virus-Host DB: RefSeq release 219

2023-06-02 version 3.6

Version of Virus-Host DB: RefSeq release 218

2023-04-03 version 3.5

Version of Virus-Host DB: RefSeq release 217

2023-02-13 version 3.4

Version of Virus-Host DB: RefSeq release 216

2022-12-9 version 3.3

Version of Virus-Host DB: RefSeq release 215

2022-11-11 version 3.2

Version of Virus-Host DB: RefSeq release 214

2022-06-20 version 3.1

Version of Virus-Host DB: RefSeq release 212

2022-04-18 version 3.0

Version of Virus-Host DB: RefSeq release 211
The upload function is updated.
New options of the alignment is available.

2022-03-14 version 2.1

Version of Virus-Host DB: RefSeq release 210

2021-12-13 version 2.0

Version of Virus-Host DB: RefSeq release 209
"Only query" mode was launched.

2021-10-04 version 1.9.1

Version of Virus-Host DB: RefSeq release 207
Selectable nucleic acid types is changed.(old version was dsDNA/ssDNA/dsRNA/ssRNA/retroviruses/satellite viruses and virophages)

2019-04-22 version 1.9

Version of Virus-Host DB: RefSeq release 93

2019-02-12 version 1.8

Version of Virus-Host DB: RefSeq release 92

2018-12-25 version 1.7

Version of Virus-Host DB: RefSeq release 91

2018-11-05 version 1.6

Version of Virus-Host DB: RefSeq release 90

2018-08-24 version 1.5

Version of Virus-Host DB: RefSeq release 89

2018-06-22 version 1.4

Version of Virus-Host DB: RefSeq release 88

2018-04-24 version 1.3

Version of Virus-Host DB: RefSeq release 87

2018-03-27 version 1.2

Version of Virus-Host DB: RefSeq release 86
New feature: gene annotaion method can be selected from prokaryotic, eukaryotic, and user defined genes.
Improved usability: the number of the max upload sequences is expanded to 50.
Improved usability: long sequence ID (up to 30 characters) is acceptable. Sequence IDs can include dots and hyphens.
Improved usability: Colors in alignment view can be customized.

2017-02-08 version 1.1

Version of Virus-Host DB: RefSeq release 76
New feature: "related" proteomic tree is available in user sessions

2017-01-04 version 1.0

Version of Virus-Host DB: RefSeq release 76
Initial release of ViPTree

Code availability

We developed ViPTreeGen, a command line tool for viral proteomic tree generation.

Reference virus data

Reference viral sequences and taxonomic information are available at Virus-Host DB.

Related work

We published a study of over thousand marine EVGs (environmental viral genomes). In the study, a prototype of the ViPTree server was developed and applied to the analysis.
Supplemental page for the study (including proteomic tree viewer and alignment viewer) can be browsed.

Citation

If you use results (data / figures) genereted by ViPTree in your research, please cite: