Multiple Sequence Alignment

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project. Platforms: Windows, Mac, Linux

BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments. Platforms: Windows, Mac, Linux

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model. Platforms: Windows, Mac, Linux

Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ Platforms: Mac, BSD, Linux

A tool to compare two Protein Sequences and show similarities with the help of dotplot. Platforms: Windows, Mac, Linux

Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet. Platforms: Windows, Mac, Linux

An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ Platforms: Mac, BSD, Linux

Sequence Logos are a common technique for visualizing the conservation of positions within a multiple sequence alignment. The technique creates an image where the height of the letter represents its sequence conservation.The Matlab bioinformatics toolbox has a function which performs this... Platforms: Matlab

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: * Is flexible enough to store all the alignment information generated by various alignment programs; * Is simple enough to be easily generated by alignment... Platforms: Mac

NGSView is a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. Platforms: *nix

The Gene Construction Kit allows graphic manipulation of DNA sequences and sophisticated plasmid drawing options. It has an award winning interface design that allows graphic manipulation of DNA sequences in addition to providing sophisticated drawing capabilities. GCK was named the "Best Plasmid... Platforms: Mac

AlleleID is a comprehensive desktop tool designed to address the challenges of pathogen detection, bacterial identification or taxa/species discrimination using microarrays and TaqMan® and molecular beacon qPCR assays. With ClustalW multiple sequence alignment at its core, AlleleID can design... Platforms: Mac

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,... Platforms: Windows

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,... Platforms: Windows

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,... Platforms: Windows, Mac, Linux

UGENE is a free cross-platform genome analysis suite. It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install. Features: * Multiple sequence alignment using MUSCLE 3, KAlign, Clustal; * HMM profiles build and search, based on the source of HMMER 2 and HMMER... Platforms: Mac

App::Session can represents a sequence of multiple events perhaps executed in separate processes. SYNOPSIS # ... official way to get a Session object ... use App; $session = App->context(); $context = $session->session(); # get the session # any of the following named parameters may be... Platforms: *nix

AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => my_blast_db, dir => $dir, fasta => my_query.fa, prog_args => V=20... Platforms: *nix

Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago,... Platforms: Mac

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and... Platforms: Mac, Java 1.5 or later