I am performing a phylogenentic analysis using specific marker genes.
I selected the aa sequences, aligned them, used as template for aligning the respective nucleotide sequences.
I created a saturation plot with the "ape" package in R, and I can see that same seq are saturated.
In order to have a more robust results I would like, now, to delete the third position in each codon.
Is there a way/program to do this?
I guess this could be done with
seq test3[seq(1, length(test3), by = 3)] # take only the first nucleotide in the codon
but I cannot find a way of taking only the first one and the second one.
I am also open to any suggestion for different way of doing this task