Package: clustalw (1.83-1.2) [non-free]

[Biology] Global multiple nucleotide or peptide sequence alignment

This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. ClustalW is very well accepted. An alternative, particularly for fragmented sequences, may be T-Coffee (http://www.ch.embnet.org/software/TCoffee.html) DIALIGN (http://dialign.gobics.de/) or one of the other many algorithms as summarised on http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html.

The output of ClustalW can be edited manually but preferably with an alignment editor like seaview or within its companion clustalx. When building a model from your alignment, this can be applied for improved database searches. The debian package hmmer creates such in form of an HMM.

 URL: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
 URL: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

Tags: Field: Biology, Implemented in: C, User Interface: Command Shell, X Window System, Role: Program, Scope: Utility, X Window System: Application