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