Usage
clustal(x, pw.gapopen = 10, pw.gapext = 0.1,
gapopen = 10, gapext = 0.2, exec = NULL,
MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE,
original.ordering = TRUE)
tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE,
original.ordering = TRUE)
Arguments
x
an object of class "DNAbin"
.
pw.gapopen, pw.gapext
gap opening and gap extension penalties
used by Clustal during pairwise alignments.
gapopen, gapext
idem for global alignment.
exec
a character string giving the name of the program, with
its path if necessary. clustal
tries to guess it depending on
the operating system (see details).
MoreArgs
a character string giving additional options.
quiet
a logical: the default is to not print on R's console the
messages from the external program.
original.ordering
a logical specifying whether to return the
aligned sequences in the same order than in x
.