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Nucleotide sequence alignment visualization software tools | High-throughput sequencing data analysis

Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments.

Source text:
(Clamp et al., 2004) The Jalview Java alignment editor. Bioinformatics, 20, 426-427.

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Geneious
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Conducts next generation sequencing (NGS) investigation. Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. It increases process efficiency and improves data organization. This tool enables the importation and conversion of a vast range of data types and offers a solution to customize researchers’ algorithms.
AliView
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An alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets.
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.
SeaView
A multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees.
Gingr
Allows users to visualize and compress trees and alignments. Gingr is a part of the Harvest suite and is compatible with standard alignment formats and can be used as general-purpose multiple alignment viewer. Besides, it also provides an interactive exploration of multiple alignments of this scale. The alignment is presented with the core-genome SNP tree, annotations and dynamic variant highlighting. Trees can be zoomed by clade or individual genomes selected to expand. Then, structural variation across the genome can also be displayed using Sybil coloring.
ALVIS
An open-source platform for the joint explorative analysis of multiple sequence alignments and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures.
STRAP / STRuctural Alignments of Proteins
A versatile workbench for protein analysis that can be used to generate and refine multiple alignments, to download PDB files from public ftp servers, visualize protein structural data with plugin or integrated protein structure viewers, and to map mutations onto three dimensional protein structures. Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs.
S2S / Sequence to Structure
Proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures. S2S can be described as a framework containing four interconnected graphical tools: a core tool (S2SViewer), a multiple sequence alignment editor (Rnalign), a secondary structure editor (Rna2DViewer) and a tertiary viewer (Rna3DViewer). Each tool has been designed to connect it to the others and to manipulate easily and efficiently the data displayed.
JDotter / Java-Dotter
Runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. It interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.
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.
MoDMaps3D / Molecular Distance Maps 3D
Computes and displays sequence and species relatedness. MoDMaps3D is an alignment-free web-tool using approximated information distance (AID) to quantify the pairwise differences in oligomer composition for all input genomic sequences, and visualizes the inter-relationships thus obtained as an interactive map in three-dimensional Euclidean space. MoDMaps3D can be used in different ways: (i) to explore a prebuilt map, (ii) to build a map ab initio for a new set of sequences, or (iii) add new DNA sequences to an existing map.
Wasabi
An open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, and it can be easily extended with other tools. Along with drag-and-drop import of local files, Wasabi can access remote data through URL and import sequence data, GeneTrees and EPO alignments directly from Ensembl.
Blixem / BLast matches In an X-windows Embedded Multiple alignment
Provides a browser for one-to-many alignment. Blixem is a web-based tool which inspect alignments of both nucleotide and amino acid sequences against a reference sequence and allows a very detailed nucleotide-level view. It can be used for investigating alignment’s quality or potential genome sequence errors and determining splice sites, polyA sites and signals or for displaying next-generation sequencing (NGS) data. The software is a part of the Seqtools toolkit.
GATA / Graphic Alignment Tool for comparative sequence Analysis
A standalone, platform independent, graphic alignment tool for comparative sequence analysis. GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file.
EzEditor
Allows manipulation of both DNA and protein sequence alignments for phylogenetic analysis. EzEditor has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes.
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.
Ribbon
Displays alignments along both reference and query sequences, along with any associated variant calls in the sample. Ribbon shows patterns in alignments of many reads across multiple chromosomes, while allowing detailed inspection of individual reads. Ribbon enables understanding of complex variants, and it may also help in the detection of sequencing and sample preparation issues, testing of aligners and variant-callers, and rapid curation of structural variant candidates. In addition to SAM and BAM files with long, short, or paired-end reads, Ribbon can also load coordinate files from whole genome aligners such as MUMmer. Therefore, Ribbon can be used to test assembly algorithms or inspect the similarity between species.
Menteric
Computes and displays views of annotated multiple alignments of the same sequences. Menteric is a visualization component available through the EnteriX resource. Users can select from five different criteria for determining conserved regions in the multiple alignment, ranging from consensus majority rule, phylogenetic distance, information content and distance from a fixed or unknown center sequence. This method also provides support for one user-specified sequence to be included in the alignment.
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