From Bioinformatics.Org Wiki
- Blixem - Blixem, which stands for "BLast matches In an X-windows Embedded Multiple alignment", is an interactive browser of pairwise BLAST matches that have been stacked up in a "master-slave" multiple alignment.
- Chimera - Excellent molecular graphics package with support for a wide range of operations, i ncluding flexible molecular graphics, high resolution images for publication, user-driven analysis, multiple sequence alignment analysis, multiple model analysis, dockin
- clustalw - The famous ClustalW multiple alignment program
- clustalx - Clustal X provides a window-based user interface to the ClustalW multiple alignment program
- DCSE - DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor
- Deep View Swiss-PdbViewer - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time
- DIALIGN - DIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residue
- ERGO - ERGO's "Pinned Regions" tool allows users to examine the chromosomal regions of a gene in other organisms which have the same structural and functional propreties as the queried gene. Also, enables alignment of AA and DNA sequences.
- gBioSeq - Biological sequence (ADN, protein) editor for GTK/Linux
- JAligner - JAligner is a Java implementation of biological sequence alignment algorithms.
- Jalview - Jalview - a java multiple alignment editor
- Mauve - Mauve is a multiple genome alignment and visualization package that considers large-scale rearrangements in addition to nucleotide substitution and indels.
- ModView - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
- Musca - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
- MUSCLE - Multiple sequence alignment. More accurate than T-Coffee, faster than CLUSTALW.
- PhyloDraw - PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
- SAM equence Alignment and Modeling Syste - a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis
- seaview - SeaView is a graphical multiple sequence alignment editor
- ShadyBox - ShadyBox The FIRST GUI based WYSIWYG multiple sequence alignment drawing program for Major Unix platforms
- xsact - EST clustering tool
- UGENE - handy visual tool for performing multiple sequence alignment using port of MUSCLE
- YASS - genomic local alignment search tool