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CView Summary
CView is an alignment visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. The relationship that sequence regions that are currently on screen have to other regions of diversity within the alignment can be observed, thus increasing intuitive insight.

Publication
Linheiro, R., Sabatino, S., Lobo, D., & Archer, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. (view)

Conference(s)
A poster that was (will be) presented at ISMB is available here.

Getting Started
There are a number of ways to obtain help in relation to CView:
1. An mp4 movie tutorial, presented by Raquel Linheiro, gives an overview of using CView and is available here. <<<<
2. The [QuickStart] page explains how to download and run the software as well as obtain test data and source code.
3. The [Help] page explains the parameter options in detail.
4. Within the software there is help available in relation to both the interface and menu items under the "Help" top menu.

Additionaly, the alignmnet used within the manuscript case study is available from the Zenodo repository here (doi no. 10.5281/zenodo.6475666).

(This is different from the small test alignment that is contained within the cview.zip file.)

Abstract
To date basic visualization of sequence alignments have largely focused on displaying per-site columns of nucleotide, or amino acid, residues along with associated frequency summarizations. The persistence of this tendency to the more recent tools designed for the viewing of mapped read data indicates that such a perspective not only provides a reliable visualization of per-site alterations, but also offers implicit reassurance to the end user in relation to data accessibility. However, the initial insight gained is limited, something that is especially true when viewing alignments consisting of many sequences representing differing factors, such as geographical location, date and subtype. A basic alignment viewer can have potential to increase initial insight through visual enhancement, whilst not delving into the realms of complex sequence analysis. Here we present CView, a visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. Within the network nodes are based on the clustering of sequence fragments spanning windows that are placed consecutively along the alignment. Edges are placed between nodes of neighbouring windows where they share sequence id’s. Thus, if a single node is selected on the network, then the relationship that all sequences passing through that node have to other regions of diversity within the alignment can be instantly observed through the tracing of paths. In addition to augmenting visual insight, CView provides many export features including variant summarization, per-site residue and kmer frequency matrixes, consensus sequence generation, alignment dissection as well as general sequence clustering, each of which are useful across a range of research areas. The software has been designed to be user friendly, intuitive and interactive. It, along with source code, a quick start guide and test data, are available through the SourceForge project page: https://sourceforge.net/projects/cview/.

Funding
This work was funded by National Funds through Portuguese Foundation for Science and Technology (FCT - Fundação para a Ciência e a Tecnologia) and FEDER through the Operational Programme for Competitiveness Factors (COMPETE) under the references POCI-01-0145-FEDER-029115 and PTDC/BIA-EVL/29115/2017.

General detail on this project are available here.

Related Software
1. CStone
2. CSReadGen
3. CView < (current location)
4. ChimSim
5. TVScript

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