The motifs found can then be used to search a sequence database to detect new members of the family. Fast and be able to align many sequences. Slow and only be able to align fewer than four sequences no more than 100 amino acid residues in length. However, it promises to find the best alignment given a scoring system. One can tune up one's existing multiple sequence alignment using hidden Markov model based alignment.
Sequences are automatically coloured according to their degree of similarity.
User can align secondary structure with the multiple sequence alignment. Incorporation of the secondary structural information can allow one to tune up one's exiting multiple sequence alignment. ClustalW is available free of charge for mac , PC and Unix . MacClade provides an interactive environment for exploring phylogeny. In MacClade's tree window, hypothesized phylogenetic trees or cladograms can be manipulated and character evolution visualized upon them.