This is the help text of the default method ClustalW. To view help
information for any of the other methods, change the 'method' argument

    msa(method="ClustalOmega", help=TRUE)
    msa(method="Muscle", help=TRUE)

or directly call the respective method with 'help=TRUE':

    msaClustalOmega(help=TRUE)
    msaMuscle(help=TRUE)


