4SALE
4SALE
Designs to handle sequence and secondary structure information of RNAs synchronously. By…
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 structure information, 4SALE enables to improve and…
Alignment-Annotator
Alignment-Annotator
A web service designed to generate interactive views of annotated nucleotide and amino…
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.
AliView
AliView
An alignment viewer and editor designed to meet the requirements of next-generation…
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…
CHROMA
CHROMA
Annotates multiple protein sequence alignments by consensus to produce formatted and…
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…
Colour INteractive Editor for Multiple Alignments
Colour INteractive Editor for Multiple Alignments
CINEMA
An interactive visual tool for the interpretation and manipulation of protein and DNA…
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. CINEMA provides a highly intuitive, flexible and…
ConStruct
ConStruct
Guides the user in correcting structurally misaligned regions. Once the initial alignment…
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…
eBioX
eBioX
A DNA sequence viewer and editor that provides a handy interface to alignment and…
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.
Geneious
Geneious
A powerful and comprehensive suite of molecular biology tools that provides visual…
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 and phylogenetic analysis. First released in 2005,…
GEnome PAir - Rapid Dotter
GEnome PAir - Rapid Dotter
Gepard
Allows the calculation of dotplots even for large sequences like chromosomes or bacterial…
Allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Gepard utilizes suffix arrays for rapid heuristic dotplot calculation. For large dotplots it searches exact word matches of a certain length (10 by…
Graphic Alignment Tool for comparative sequence…
Graphic Alignment Tool for comparative sequence Analysis
GATA
A standalone, platform independent, graphic alignment tool for comparative sequence…
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…
Jalview
Jalview
A system for interactive WYSIWYG editing, analysis and annotation of multiple sequence…
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…
JEvTrace
JEvTrace
A Java application implementing the evolutionary trace (ET) method and its variations.…
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…
MacVector
MacVector
A comprehensive Macintosh application that provides sequence editing, primer design,…
A comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis and a variety…
Pictogram
Pictogram
A handy tool to help you visualize sequence alignments and consensus sequences. Input…
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 frequencies of the bases at each position. You can specify…
Protein Family Alignment Annotation Tool
Protein Family Alignment Annotation Tool
PFAAT
A Java application that allows one to edit, analyze, and annotate multiple sequence…
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.
SeaView
SeaView
A multiplatform program designed to facilitate multiple alignment and phylogenetic tree…
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…
SemiAutomated RNA Sequence Editor
SemiAutomated RNA Sequence Editor
SARSE
A graphical sequence editor for working with structural alignments of RNA. The editor…
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 introduction of errors when doing alignment editing. SARSE…
Sequence to Structure
Sequence to Structure
S2S
Proposes a framework in which an user can easily display, manipulate and interconnect…
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…
SnipViz
SnipViz
A drop-in client-side module for web sites designed to efficiently visualize and…
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…
STRuctural Alignments of Proteins
STRuctural Alignments of Proteins
STRAP
A versatile workbench for protein analysis that can be used to generate and refine…
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…
Visualize Structure Sequence Alignment
Visualize Structure Sequence Alignment
VISSA
An integrated multiple alignment and 3D structure visualization program that can (1) map…
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 alignment of preselected, key residues. VISSA also has…