Multipe Sequence Alignments:
Use the same dataset to produce an alignment with Muscle
Use the same dataset to produce an alignment with ClustalW
Compare The alignments: are they identical?
Use the Mcoffee mode on the T-Coffee server to combine a Kalign, T-Coffee and Muscle MSA
Examine the colored output (html) and compare it with the differences you had observed in the previous sequences
Questions should be sent to C.Notredame