Question: Reduce saturation by deleting the 3rd position in each codon of DNA seqs. R ape package
gravatar for dago
5.1 years ago by
dago2.6k wrote:

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


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


dna alignment R phylogeny • 2.3k views
ADD COMMENTlink modified 5.1 years ago by David W4.7k • written 5.1 years ago by dago2.6k
gravatar for David W
5.1 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

In R you can use negative indices to exclude elements. 


Here's an exmaple using one of ape's datasets (not this is an alignment (matrix), not a single sequence (vector) as in your example


ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by David W4.7k

Ok, really good thanks!

ADD REPLYlink written 5.1 years ago by dago2.6k

I might not understand the command AlignmentToFilter[, -seq(1, ncol(AlignmentToFilter), by=3) ] .. but it is apparently skipping the first codon position in my hand while command AlignmentToFilter[, -seq(3, ncol(AlignmentToFilter), by=3) ] worked for me and omitted the 3rd codon position.

ADD REPLYlink written 2.6 years ago by al-ash140
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