Viewing multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visualize conservation across protein families as well as unusual features of particular sequences.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Renders sequence similarities and secondary structure information for analysis and publication purposes. ESPript can assist users to optimize an alignment thank to its capability to display on the same figure the secondary structure information of each aligned sequence. It allows users to obtain an output from different files of aligned sequences. This tool is able to return the temperature factors replaced by similarity scores that it calculates.
Allows users to perform the alignment of multiple related sequences. MultAlin is a platform based on an algorithm exploiting progressive pairwise alignment that considers relationships that can exist among some subsets of sequences. The application includes options to set the desired output format and its size and colors as well as configure personalized alignment parameters such as the number of iterations and the gap penalties required.
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.
Provides a prettyprint multiple alignment output or DNA sequences. BoxShade does not make the alignment by itself and need a preprocessed file or a multiple file editor. This software allows users to customize, among others, the applied shading, sequence numbering or consensus output. It works in two steps: the first is the checking for every column in the alignment and the second verifies the residue and the consensus of the corresponding alignment column.
Allows visualization of pairwise sequence similarities in 2D or 3D spaces. CLANS is an application based on the Fruchterman–Reingold graph layout algorithm. The software performs all-against-all BLAST searches and calculates pairwise attraction values based on the high scoring segment pair (HSP) P-values. Users can rotate, translate and zoome the graph showing all pairwise interactions to better see sequence relationships. They can also add, extract or remove sequence from graphs.
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 is also a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.