Multipe Sequence Alignments:

You are given the following sequences.

  1. Generate a default clustalW alignment, using the interactive menu and the prompt. How many files does clustalw produce

  2. Obtain a list of the command line parameters (clustalw -options). Consult the online documentation at the ebi [DOC]

  3. Gap Penalties : change the gap opening penalties. Are the alignments different ?

  4. Matrices : change the matrix.

  5. Guide Tree : invert the order in which the sequences 1thm and sepr_thesp are incorporated in the alignment

  6. Phylogenic Tree:Compute a phylogenetic tree using ClustalW and your alignment

  7. Reference aln :Compare this alignment with its BaliBase reference ref.