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Sequence alignment visualization software tools

Viewing multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visualize conservation across protein families as well as unusual features of particular sequences.

Source text:
(Martin, 2014) Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV). F1000Res.

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ANTHEPROT
Allows protein sequence analysis. ANTHEPROT is able to interactively couple multiple alignments with secondary structure predictions. It can submit tasks on a remote server and retrieve data from a remote Web server. This tool is a complete solution for Intranet protein sequence analysis for universities, biological research institutes or biomedical companies. It permits users to integrate secondary structure predictions within multiple alignment and full interactive editing of alignments.
TnT / Trees and Tracks
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Consists of a set of libraries aimed at creating configurable and interactive re-usable visualizations of trees and track-based annotations. TnT is able to generate tree- and track-based visualizations for the web. The platform also provides an API that allows the development of many different visualizations ranging from simple species trees to complex visualizations comprising per-node data annotations.
Jalview
A system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.
MSAViewer
A quick and easy visualization and analysis JavaScript component for multiple sequence alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is “web ready”: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. As part of BioJS, the MSAviewer can interoperate with a growing set of biological data viewers. The phylogenetic tree and the sequence logo viewers are already integrated in the current release.
MODalign
An interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). MODalign interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information.
Protael
A JavaScript library for creating interactive visualizations of biological sequences and various associated data. Protael allows users to generate high-quality vector graphics (SVG) and integrate it into web pages. Protael is capable of displaying multiple data types, such as sequence annotations, substitutions, posttranslational modifications, cleavage sites, disulfide bridges, various types of quantitative data, and alignments with known structures. Sequence features, annotations, quantitative data and aligned sequences can occupy multiple data tracks.
PeptideMapper
Indexes and queries proteomes. PeptideMapper is a very efficient and versatile approach. This method is particularly well-suited for challenging experimental setups involving large databases. It has the potential to overcome several bottlenecks in proteomic data analysis workflows and is especially equipped for the handling of de novo sequencing results. PeptideMapper is easily implementable in both server and desktop applications, either via command line or as external library.
SnipViz
A drop-in client-side module for web sites designed to efficiently visualize and disseminate gene and protein sequences. SnipViz has a space-efficient, interactive, and dynamic interface for navigating, analyzing and visualizing sequence data. It is written using standard World Wide Web technologies (HTML, Javascript, and CSS) and is compatible with most web browsers. SnipViz is designed as a modular client-side web component and may be incorporated into virtually any web site and be implemented without any programming.
AlignmentViewer
Assists users in visualizing and analyzing protein multiple sequence alignment. AlignmentViewer complements multiple sequence alignment (MSA) tools and provides: (i) in-browser and serverless execution, (ii) visualization of very large MSAs, (iii) exploration of conservation patterns, (iv) sequence filtering, (v) logo display, (vi) pairwise sequence identity map (vii) spring-directed 2D-layout of protein distribution in sequence space (planned) and (viii) display of top-ranked evolutionary couplings.
CLANS / CLuster ANalysis of Sequences
Obsolete
Allows visualization of pairwise sequence similarities in 2D or 3D spaces. CLANS is an application based on the Fruchterman–Reingold graph layout algorithm. The software performs all-against-all BLAST searches and calculates pairwise attraction values based on the high scoring segment pair (HSP) P-values. Users can rotate, translate and zoome the graph showing all pairwise interactions to better see sequence relationships. They can also add, extract or remove sequence from graphs.
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