Generate a default clustalW alignment, using the interactive menu and the prompt. How many files does clustalw produce
Obtain a list of the command line parameters (clustalw -options). Consult the online documentation at the ebi [DOC]
Gap Penalties : change the gap opening penalties. Are the alignments different ?
Matrices : change the matrix.
Guide Tree : invert the order in which the sequences 1thm and sepr_thesp are incorporated in the alignment
Phylogenic Tree:Compute a phylogenetic tree using ClustalW and your alignment
Reference aln :Compare this alignment with its BaliBase reference ref.