clustalw | global multiple nucleotide or peptide sequence alignment | Mehr ...
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. Clustal W is very well accepted. . The output of Clustal W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal X. 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. . For details and citation purposes see paper "Clustal W and Clustal X version 2.0", Larkin M., et al. Bioinformatics 2007 23(21):2947-2948
