install.packages('ape', repos='http://cran.wustl.edu/') install.packages('seqinr', repos='http://cran.wustl.edu/') library(ape) library(seqinr) reverse.align(nucl.file = 'Parul_dna_fasta.muscle2.fas', protaln.file = 'Parul_protein_fasta.muscle', input.format = 'fasta', out.file = 'codonAlignment.txt', output.format = 'fasta', align.prot = FALSE, numcode = 1, clustal.path = NULL, forceDNAtolower = TRUE, forceAAtolower = FALSE) codondata = read.alignment('codonAlignment.txt', format="fasta") kaks(codondata)