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Nucleotide sequence alignment visualization software tools | Comparative genomics

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.…
TnT
Desktop

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…

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…

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…

Gingr
Desktop

Gingr

Allows users to visualize and compress trees and alignments. Gingr is a part of…

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…

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…

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…

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…

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…

Kablammo
Web

Kablammo

Produces vector-based visualizations of sequence alignments generated by BLAST.…

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…

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…

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.

MoDMaps3D
Web

MoDMaps3D Molecular Distance Maps 3D

Computes and displays sequence and species relatedness. MoDMaps3D is an…

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…

AAScatterPlot
Desktop

AAScatterPlot

Permits to monitor the evolution of hemagglutinin cleavage site in H9 avian…

Permits to monitor the evolution of hemagglutinin cleavage site in H9 avian viruses. AAScatterPlot compacts information about the hydropathy index, Van der Waals volume, chemical property, and…

gff2aplot
Desktop

gff2aplot

Generates two-dimensional (2D) annotated alignment plots in PostScript format.…

Generates two-dimensional (2D) annotated alignment plots in PostScript format. gff2aplot can serve as a visualization filter after running some independent alignment tool. It parses alignment…

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…

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,…

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…

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,…

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…

G T A T C G C T A
Geneious
Desktop

Geneious

Proposes a powerful and comprehensive suite of next generation sequencing (NGS)…

Proposes a powerful and comprehensive suite of next generation sequencing (NGS) analysis tools. Through an intuitive and user-friendly interface, Geneious provides visual sequence alignment and…

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…

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.…

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…

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…

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…

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…

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…

AlignmentViewer
Web

AlignmentViewer

Alignment viewer with BioJS MSA Viewer. AlignmentViewer is a part of HH-suite…

Alignment viewer with BioJS MSA Viewer. AlignmentViewer is a part of HH-suite software.

prettyplot
Desktop

prettyplot

Draws a sequence alignment with pretty formatting. prettyplot draws a plot of…

Draws a sequence alignment with pretty formatting. prettyplot draws a plot of the input sequence alignment. The sequences are rendered in pretty formatting on the specified graphics device. The tool…

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…

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…

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…

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…

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.

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