- \item{x}{a matrix or a list containing the DNA sequences.}
- \item{model}{a character string specifying the evlutionary model to be
- used; must be one of \code{"raw"}, \code{"N"}, \code{"JC69"},
- \code{"K80"} (the default), \code{"F81"}, \code{"K81"},
- \code{"F84"}, \code{"BH87"}, \code{"T92"}, \code{"TN93"},
- \code{"GG95"}, \code{"logdet"}, or \code{"paralin"}.}
+ \item{x}{a matrix or a list containing the DNA sequences; this must be
+ of class \code{"DNAbin"} (use \code{\link{as.DNAbin}} is they are
+ stored as character).}
+ \item{model}{a character string specifying the evolutionary model to be
+ used; must be one of \code{"raw"}, \code{"N"}, \code{"TS"},
+ \code{"TV"}, \code{"JC69"}, \code{"K80"} (the default),
+ \code{"F81"}, \code{"K81"}, \code{"F84"}, \code{"BH87"},
+ \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"},
+ \code{"paralin"}, \code{"indel"}, or \code{"indelblock"}.}