I am pretty new to R. So I apologize for asking maybe a very basic question. Let's say I have a fasta file with sequence below:


Is there a function or method to calculate entropy for each column in R? I did some research and found a function that calculate entropy for Amino Acids but not for DNA nucleotides.

I would like to have the output be stored in a vector or in a list.

Thanks for the help in advance!

  • 1
    $\begingroup$ Hi what is the goal of your research? Entropy is a function of a given allele since you have variation, particularly indels this is not possible. With an indel position e.g. 4 now becomes position 3 (sequence_2) within an entropy calculation, so which column are you referirng to? I think you are confusing this with phylogenetic methods. $\endgroup$
    – M__
    Commented Jun 27, 2020 at 5:57
  • $\begingroup$ Hi Michael, I was able to get it to with some other people's help. But to answer your question, The MolecularEntropy function in R did exactly what wanted to. It calculated the entropy at each nucleotide position with aligned sequences. $\endgroup$
    – Xiaoxixi
    Commented Jun 27, 2020 at 15:26
  • $\begingroup$ okay, the blurb does say "Gaps are ignored on a site by site basis so the entropy values may have different number of observations among sites." It also needs sequences to be the same length ... I personally don't think it works with indels $\endgroup$
    – M__
    Commented Jun 27, 2020 at 15:29


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.