Reduce saturation by deleting the 3rd position in each codon of DNA seqs. R ape package

Question

[dago]

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

Answer 1

[David W]

In R you can use negative indices to exclude elements.

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

 library(ape)
 data(woodmouse)
 #Just the third codon (assuming alignment is in-frame)
 woodmouse[, seq(1, ncol(woodmouse), by=3) ]

## 15 DNA sequences in binary format stored in a matrix.
## 
## All sequences of same length: 322 
## 
## Labels: No305 No304 No306 No0906S No0908S No0909S ...
## 
## Base composition:
##     a     c     g     t 
## 0.285 0.238 0.219 0.258

 #skipping the thrid codon
 woodmouse[, -seq(1, ncol(woodmouse), by=3) ]

## 15 DNA sequences in binary format stored in a matrix.
## 
## All sequences of same length: 643 
## 
## Labels: No305 No304 No306 No0906S No0908S No0909S ...
## 
## Base composition:
##     a     c     g     t 
## 0.318 0.273 0.079 0.330

view raw gist.md hosted with ❤ by GitHub

[dago]

Ok, really good thanks!

[al-ash]

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.