DNA sequence Alignment Using the program PRANK.
prank(x, outfile, guidetree = NULL, gaprate = 0.025,
gapext = 0.75, path)an object of class DNAbin.
a character string giving a name for the output file.
an object of class phylo to be used as guidetree in alignment.
numeric giving the gap opening rate; defaults to 0.025.
numeric giving the gap extension penalty; defaults to 0.75.
a character string indicating the path to the PRANK executable.
matrix of class "DNAbin"
read.fas to import DNA sequences;
mafft for another alignment algorithm;
gblocks and aliscore for alignment cleaning.