text: user3704: I have an alignment of some full genome sequences of DENV1 that we have recently sequenced from the serum of patients. I have already cleaned the sequences, built the alignments and done the SNPs calling. After that I got the consensus sequences from each sample and I used MEGA to build the alignments of the consensus sequences and to construct a tree etc.
  From just looking the alignment of the consensus sequences I can see several nt s differences among the sequences. 
  Does anyone know if you can export from MEGA like a sort of table where you could see the nt changes for each position and sample?
  
  user1642: You don't say which version of MEGA you are using, but this works for MEGA X on Linux:
  
  Open your alignment with the "Sequence data explorer"
  At the "Highlight" menu, select "Variable sites".
  Then at the menu "Statistics", select "Use only highlighted sites" and select what you consider an appropriate output - I choose "Display results as CSV".
  Now at the menu "Data" select "Export data"; at the "Sequence data export options window" if necessary select the data format again, and select "For each site" at "Writing site numbers", and select "Only highlighted sites" at "Selected sites to include".
  
  This will result in a comma-separated values file, showing only positions with variable sites.
  
original_text: 3704: <p>I have an alignment of some full genome sequences of DENV1 that we have recently sequenced from the serum of patients. I have already cleaned the sequences, built the alignments and done the SNPs calling. After that I got the consensus sequences from each sample and I used MEGA to build the alignments of the consensus sequences and to construct a tree etc.</p>
  
  <p>From just looking the alignment of the consensus sequences I can see several nt s differences among the sequences. </p>
  
  <p>Does anyone know if you can export from MEGA like a sort of table where you could see the nt changes for each position and sample?</p>
   1642: <p>You don't say which version of MEGA you are using, but this works for MEGA X on Linux:</p>
  
  <ol>
  <li><p>Open your alignment with the "Sequence data explorer"</p></li>
  <li><p>At the "Highlight" menu, select "Variable sites".</p></li>
  <li><p>Then at the menu "Statistics", select "Use only highlighted sites" and select what you consider an appropriate output - I choose "Display results as CSV".</p></li>
  <li><p>Now at the menu "Data" select "Export data"; at the "Sequence data export options window" if necessary select the data format again, and select "For each site" at "Writing site numbers", and select "Only highlighted sites" at "Selected sites to include".</p></li>
  </ol>
  
  <p>This will result in a comma-separated values file, showing only positions with variable sites.</p>
  