<p>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:</p>
<pre><code>&gt;sequence_1
ACCTGC--A
&gt;sequence_2
ACC-GCTTA
&gt;sequence_3
ACCTGCTTA
</code></pre>
<p>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.</p>
<p>I would like to have the output be stored in a vector or in a list.</p>
<p>Thanks for the help in advance!</p>

CC BY-SA 4.0
2020-06-27T05:57:06.603Z
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.
M__
CC BY-SA 4.0
2020-06-27T15:26:24.230Z
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.
Xiaoxixi
CC BY-SA 4.0
2020-06-27T15:29:07.883Z
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
M__
<r><phylogenetics>
Calculate Entropy for DNA Multiple Sequence Alignment in R
# Calculate Entropy for DNA Multiple Sequence Alignment in R

(Asked by: username_0 on 2020-06-27)

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:
>sequence_1
ACCTGC--A
>sequence_2
ACC-GCTTA
>sequence_3
ACCTGCTTA

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!

**Tags:** r, phylogenetics
> **Comments:**
> **username_1**: 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.  
> **username_0**: 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.  
> **username_1**: 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  

---

## 0 answers

