Answers.Body: <p>I think there needs to be clarification of the question. Shannon entropy is not the same thing as the Shannon-Wiener diversity index (H), commonly referred to as the Shannon index.</p>
  
  <p>The reason I brought it up is because you have the tag "population genetics". Shannon diversity index is commonly used in population genetics to compare species richness (the number of species in a given area) and their relative abundance.</p>
  
  <p>Shannon entropy is more to do protein structure, which isn't really population genetics, but can relate to how stable a given mutation might be. That is not really population genetics however, population genetics is about abundance of a given allele in this context. </p>
  
  <p>I am pretty sure that on this site most responders will recommend alternative free energy approaches to perform this style of analysis.</p>
  
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Answers.CreationDate: 2020-03-24T16:31:03.643Z
Answers.Text: Thank you so much for your response. I totally agree with you. That was a wrong tag to place for the question i asked. I have also done some reading and realized that Shannon entropy and Shannon-Wienner diversity index are two different things. So I seeked clarification from my supervisor and he actually meant Shannon index and not Shannon entropy as he advised me before. What do i want to do; I have sequence data for viruses from different outbreaks. My plan is to divide the sequences from each outbreak into ; early, mid-phase and late phase. Then use shannon index as a measure of diversity.
Answers.UserDisplayName: henrick kola
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Answers.Text: Okay thanks, given the error here, it might be better to simply ask a new question. The "population genetics" was correct, but "entropy" was wrong.
Answers.UserDisplayName: M__
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Answers.Text: How is Shannon-Wiener diversity index https://en.wikipedia.org/wiki/Diversity_index#Shannon_index any different from Shannon entropy? They are mathematically exactly the same.
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Body: <p>I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do  not understand the concept of shannon entropy. Would anyone explain please how it works or advise on some resources i can use to understand shannon entropy.</p>
  
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Comments.CreationDate: 2020-03-23T13:28:32.160Z
Comments.Text: There are certainly protein structural biologists on the site that could do this, however I doubt they would recommend this as a key strategy to understand the entropy of spatial relationships
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny><r><genomics><population-genetics>
Title: How to compute Shanon entropy
ThreadText: # How to compute Shanon entropy
  
  (Asked by: username_0 on 2020-03-23)
  
  I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how it works or advise on some resources i can use to understand shannon entropy.
  
  **Tags:** phylogenetics, phylogeny, r, genomics, population-genetics
  
  > **Comments:**
  > **username_1**: There are certainly protein structural biologists on the site that could do this, however I doubt they would recommend this as a key strategy to understand the entropy of spatial relationships  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-03-23. Score: 2
  
  I think there needs to be clarification of the question. Shannon entropy is not the same thing as the Shannon-Wiener diversity index (H), commonly referred to as the Shannon index.
  
  The reason I brought it up is because you have the tag "population genetics". Shannon diversity index is commonly used in population genetics to compare species richness (the number of species in a given area) and their relative abundance.
  
  Shannon entropy is more to do protein structure, which isn't really population genetics, but can relate to how stable a given mutation might be. That is not really population genetics however, population genetics is about abundance of a given allele in this context.
  
  I am pretty sure that on this site most responders will recommend alternative free energy approaches to perform this style of analysis.
  
  > **Comments:**
  > **username_0**: Thank you so much for your response. I totally agree with you. That was a wrong tag to place for the question i asked. I have also done some reading and realized that Shannon entropy and Shannon-Wienner diversity index are two different things. So I seeked clarification from my supervisor and he actually meant Shannon index and not Shannon entropy as he advised me before. What do i want to do; I have sequence data for viruses from different outbreaks. My plan is to divide the sequences from each outbreak into ; early, mid-phase and late phase. Then use shannon index as a measure of diversity.  
  > **username_1**: Okay thanks, given the error here, it might be better to simply ask a new question. The "population genetics" was correct, but "entropy" was wrong.  
  > **username_2**: How is Shannon-Wiener diversity index https://en.wikipedia.org/wiki/Diversity_index#Shannon_index any different from Shannon entropy? They are mathematically exactly the same.  
  
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