Answers.Body: <p>In short I'm afraid it isn't possible because you lose the linkage per Haplotype which is the core information and vital for any population genetics or phylogenetic analysis.</p>
  <p>Position-specific scoring matrix e.g. A .60 C .20 G .20 T 0
  I tried to produce a position scoring matrix, but it didn't work out, anyway the allele frequency for each e.g. amino acid are given for each alignment position.</p>
  <p>You could produce a consensus sequence which, albeit be hypothetical, it might be of some use to understand the generic behaviour of all the sequences in your sample.</p>
  <p>Here's a cartoon describing linkage and its importance,</p>
  <p><a href="https://i.sstatic.net/xanov.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/xanov.png" alt="enter image description here" /></a></p>
  <p>For a multiple sequence alignment of course AB and ab are amino acid residues within the same locus. PSSM could be used to construct a matrix to analyses an established alignment, but that's a fairly complicated Phylogenetics calculation (and a separate question).</p>
  
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Answers.CreationDate: 2022-03-19T13:27:24.890Z
Answers.Text: Thank you for the explanation from the perspective of linkage!
Answers.UserDisplayName: Johnny Tam
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Answers.CreationDate: 2022-03-19T13:30:34.723Z
Answers.Text: You are very welcome @JohnnyTam let me know if you have further questions (posted separately of course as per SE rules).
Answers.UserDisplayName: M__
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Answers.CreationDate: 2022-03-18T10:18:47.470Z
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Body: <p>I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from  a position-Specific Scoring Matrices (PSSM).</p>
  <p>Is it possible? I suppose co-evolution information is lost in PSSM so maybe it is difficult?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-19T00:00:57.290Z
Comments.Text: I edited the question to explain what the acronyms represented.
Comments.UserDisplayName: M__
Tags: <phylogenetics><proteins><phylogeny><pssm>
Title: Is it possible to reconstruct an MSA with PSSM?
ThreadText: # Is it possible to reconstruct an MSA with PSSM?
  
  (Asked by: username_0 on 2022-03-18)
  
  I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from a position-Specific Scoring Matrices (PSSM).
  
  Is it possible? I suppose co-evolution information is lost in PSSM so maybe it is difficult?
  
  **Tags:** phylogenetics, proteins, phylogeny, pssm
  
  > **Comments:**
  > **username_1**: I edited the question to explain what the acronyms represented.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-03-18. Score: 1 | Accepted answer
  
  In short I'm afraid it isn't possible because you lose the linkage per Haplotype which is the core information and vital for any population genetics or phylogenetic analysis.
  
  Position-specific scoring matrix e.g. A .60 C .20 G .20 T 0
  I tried to produce a position scoring matrix, but it didn't work out, anyway the allele frequency for each e.g. amino acid are given for each alignment position.
  
  You could produce a consensus sequence which, albeit be hypothetical, it might be of some use to understand the generic behaviour of all the sequences in your sample.
  
  Here's a cartoon describing linkage and its importance,
  
  [![enter image description here](https://i.sstatic.net/xanov.png)](https://i.sstatic.net/xanov.png)
  
  For a multiple sequence alignment of course AB and ab are amino acid residues within the same locus. PSSM could be used to construct a matrix to analyses an established alignment, but that's a fairly complicated Phylogenetics calculation (and a separate question).
  
  > **Comments:**
  > **username_0**: Thank you for the explanation from the perspective of linkage!  
  > **username_1**: You are very welcome @username_0 let me know if you have further questions (posted separately of course as per SE rules).  
  
  ---
  
  