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.
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.
Provides a web platform for comparing genomic sequences across related species. Phylo-VISTA can (1) produce multiple sequence alignments, (2) visualize the results in the context of existing annotation and (3) analyze comparative results in search for important sequence signals in alignments. This software consists of four components: a phylogenetic tree, a sequence traversal panel, similarity plots and a text window.
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.
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.
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.
Allows comparative views of a reference bacterial or virus genome with sequences from several related organisms. EnteriX consists of three tools for graphically portraying alignment information: Enteric and Menteric. It provides to users the ability to select the genomes to be included in the views from among those available in the data store. Its main goal is to present alignment information and inferred or associated properties in an integrated framework and as an instrument for discovery and analysis.
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.
A Java application implementing the evolutionary trace (ET) method and its variations. These methods have in common the analysis of protein families through MSAs, phylogenetic trees and protein structures. The ET method has proved a useful tool for understanding the sequential and structural aspects of protein function, including the analysis of variations relevant to molecular specificity.
Guides the user in correcting structurally misaligned regions. Once the initial alignment is refined, ConStruct is able to predict secondary as well as tertiary consensus structures with high sensitivity and specificity. ConStruct’s graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints.
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.
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.
A Java application that allows one to edit, analyze, and annotate multiple sequence alignments. The annotation features are a key component as they provide a framework to for further sequence, structure and statistical analysis.
Allows users to view and edit multiple sequence alignments and phylogenic trees in a wide range of formats thanks to a Scoredist algorithm. Belvu generates configurable colour schemes or distance matrices between sequences and build distance-based trees. It integrates automatic editing operations and an extended command-line mode. The software can easy be integrated in software pipelines and is a part of the Seqtools toolkit.
Annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. CHROMA is designed to be flexible and reliable, and has a simple-to-use graphical user interface.
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.
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.
Produces vector-based visualizations of sequence alignments generated by BLAST. Kablammo analyzes BLAST XML files uploaded by the user. The result can be viewed directly into Kablammo, which gives a rapid visual overview of BLAST results. The Kablammo visualizations may illustrate many features, like shared protein domains, chromosome structural modifications and genome misassembly.