Answers.Body: <p>I guess you already know what identity means. But for completeness, it is the % of pairwise alignment position which have an identical amino acid residue. For the identity+similarity it is important to know that amino acids can be grouped according to their physicochemical properties e.g. charge, size etc. While there are standard groupings for amino acids it may be that the proprietary algorithm uses different groupings. Either way, % identity+similarity would imply the number of pairwise alignment positions which contain either the same amino acid or amino acids from the same group (however they define groups).</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-21T23:06:08.790Z
Answers.LastActivityDate: 2017-08-21T23:06:08.790Z
Answers.UserDisplayName: Nathan S. Watson-Haigh
Body: <p>I am helping a colleague to interpret protein multiple sequence alignment results. My colleague used a third-party proprietary solution (I know...) to calculate the alignment, and one of the resulting tables is a pairwise distance matrix with identity % in the top triangle and <strong>identity plus similarity</strong> in the bottom triangle. </p>
  
  <p>I am struggling to interpret identity plus similarity, despite the fact I found the metric in several papers. </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-21T18:59:32.857Z
Comments.Text: A guess; Identity: the amino acids that are equal. Similarity: The amino acids of the same group.
Comments.UserDisplayName: llrs
Tags: <proteins><phylogenetics>
Title: Identity plus Similarity Interpretation
ThreadText: # Identity plus Similarity Interpretation
  
  (Asked by: username_0 on 2017-08-21)
  
  I am helping a colleague to interpret protein multiple sequence alignment results. My colleague used a third-party proprietary solution (I know...) to calculate the alignment, and one of the resulting tables is a pairwise distance matrix with identity % in the top triangle and **identity plus similarity** in the bottom triangle.
  
  I am struggling to interpret identity plus similarity, despite the fact I found the metric in several papers.
  
  **Tags:** proteins, phylogenetics
  
  > **Comments:**
  > **username_1**: A guess; Identity: the amino acids that are equal. Similarity: The amino acids of the same group.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2017-08-21. Score: 3
  
  I guess you already know what identity means. But for completeness, it is the % of pairwise alignment position which have an identical amino acid residue. For the identity+similarity it is important to know that amino acids can be grouped according to their physicochemical properties e.g. charge, size etc. While there are standard groupings for amino acids it may be that the proprietary algorithm uses different groupings. Either way, % identity+similarity would imply the number of pairwise alignment positions which contain either the same amino acid or amino acids from the same group (however they define groups).
  
  
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