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…
Jalview
Desktop

Jalview

A system for interactive WYSIWYG editing, analysis and annotation of multiple…

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…

AliView
Desktop

AliView

An alignment viewer and editor designed to meet the requirements of…

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…

MView
Web
Desktop

MView

Reformats the results of a sequence database search (BLAST, FASTA, etc) or a…

Reformats the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc…) adding optional HTML markup to control colouring and web page layout. MView…

BLAST Viewer
Desktop

BLAST Viewer

Aims at displaying in a graphical way results from the NCBI BLAST software. The…

Aims at displaying in a graphical way results from the NCBI BLAST software. The BlastViewer Tool offers a graphical interface to the Basic Local Alignment Search Tool. NCBI BLAST finds regions of…

JAE
Desktop

JAE Jemboss Alignment Editor

Incorporates standard methods of editing, and colouring residues and…

Incorporates standard methods of editing, and colouring residues and nucleotides to highlight important regions of interest. JAE can be used interactively to edit a sequence alignment. It can be used…

MACAW
Desktop

MACAW Multiple Alignment Construction & Analysis Workbench

Allows the user to construct multiple alignments by locating, analyzing,…

Allows the user to construct multiple alignments by locating, analyzing, editing and combining “blocks” of aligned sequence segments. MACAW includes sequence alignment search, editing and…

BlasterJS
Desktop

BlasterJS

A free to use, open source Javascript BLAST alignments viewer library.…

A free to use, open source Javascript BLAST alignments viewer library. BlasterJS offers support for both single and multiple alignments. This library allows (i) to display BLAST hits distribution in…

Ribbon
Web
Desktop

Ribbon

Displays alignments along both reference and query sequences, along with any…

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,…

MSAViewer
Web

MSAViewer

A quick and easy visualization and analysis JavaScript component for multiple…

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…

ALVIS
Desktop

ALVIS

An open-source platform for the joint explorative analysis of multiple sequence…

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…

Wasabi
Web
Desktop

Wasabi

An open source, web-based environment for evolutionary sequence analysis.…

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…

TnT
Library

TnT

A set of libraries aimed at creating powerful tree- and track-based…

A set of libraries aimed at creating powerful tree- and track-based visualisations for the web. Its modularity and rich API facilitate the development of many different visualisations ranging from…

GATA
Desktop

GATA Graphic Alignment Tool for comparative sequence Analysis

A standalone, platform independent, graphic alignment tool for comparative…

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…

SnipViz
Desktop

SnipViz

A drop-in client-side module for web sites designed to efficiently visualize…

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…

Pictogram
Web

Pictogram

A handy tool to help you visualize sequence alignments and consensus sequences.…

A handy tool to help you visualize sequence alignments and consensus sequences. Input your short DNA sequences, and the web server will create an image like that above, showing the relative…

4SALE
Desktop

4SALE

Designs to handle sequence and secondary structure information of RNAs…

Designs to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary…

CHROMA
Desktop

CHROMA

Annotates multiple protein sequence alignments by consensus to produce…

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…

ConStruct
Desktop

ConStruct

Guides the user in correcting structurally misaligned regions. Once the initial…

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…

MacVector
Desktop

MacVector

A comprehensive Macintosh application that provides sequence editing, primer…

A comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic…

SARSE
Desktop

SARSE SemiAutomated RNA Sequence Editor

A graphical sequence editor for working with structural alignments of RNA. The…

A graphical sequence editor for working with structural alignments of RNA. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the…

S2S
Desktop

S2S Sequence to Structure

Proposes a framework in which an user can easily display, manipulate and…

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…

CINEMA
Desktop

CINEMA Colour INteractive Editor for Multiple Alignments

An interactive visual tool for the interpretation and manipulation of protein…

An interactive visual tool for the interpretation and manipulation of protein and DNA sequences. CINEMA allows the user to interactively construct and edit and visualise multiple sequence alignments.…

PFAAT
Desktop

PFAAT Protein Family Alignment Annotation Tool

A Java application that allows one to edit, analyze, and annotate multiple…

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,…

SeaView
Desktop

SeaView

A multiplatform program designed to facilitate multiple alignment and…

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…

Alignment-Annot…
Web

Alignment-Annotator

A web service designed to generate interactive views of annotated nucleotide…

A web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software.

JEvTrace
Desktop

JEvTrace

A Java application implementing the evolutionary trace (ET) method and its…

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…

STRAP
Desktop

STRAP STRuctural Alignments of Proteins

A versatile workbench for protein analysis that can be used to generate and…

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…

G T A T C G C T A
Geneious
Desktop

Geneious

A powerful and comprehensive suite of molecular biology tools that provides…

A powerful and comprehensive suite of molecular biology tools that provides visual sequence alignment and editing, sequence assembly with a clear graphical interface, comprehensive molecular cloning…

EzEditor
Desktop

EzEditor

Allows manipulation of both DNA and protein sequence alignments for…

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…

eBioX
Desktop

eBioX

A DNA sequence viewer and editor that provides a handy interface to alignment…

A DNA sequence viewer and editor that provides a handy interface to alignment and assembly programs. eBioX is an easy to use open source program incorporating multiple bioinformatics utilities.

VISSA
Desktop

VISSA Visualize Structure Sequence Alignment

An integrated multiple alignment and 3D structure visualization program that…

An integrated multiple alignment and 3D structure visualization program that can (1) map and highlight residues from a 1D alignment onto a 3D structure and vice versa and (2) display only the…

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