Merge two or more DNA or amino acid sequence alignments by profile alignment with MAFFT.
mafft.merge(subMSA, method = "auto", gt, thread = -1, exec,
quiet = TRUE)A character string giving the alignment method. Available
accuracy-oriented methods for less than 200 sequences are
"localpair", "globalpair", and "genafpair";
"retree 1" and "retree 2" are for speed-oriented alignment.
The default is "auto", which lets MAFFT choose an appropriate
alignment method.
An object of class phylo that is to be used as a
guide tree during alignment.
Integer giving the number of physical cores MAFFT should use;
with thread = -1 the number of cores is determined automatically.
A character string giving the path to the MAFFT executable
including its name, e.g. something like /user/local/bin/mafft under
UNIX-alikes.
Logical, if set to TRUE, mafft progress is printed out on
the screen.