text: user14169: 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?
  
  user3848: 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,
  
  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).
  
original_text: 14169: <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>
   3848: <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.stack.imgur.com/xanov.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
  