text: user14295: I am performing  multiple sequence alignment using Clustal Omega for 600 RNA covid-sequences, i.e. cDNA on Genbank, with input characters around 30574 characters for each sequence.
  I am running it on windows cmd.
  I defined parameters in input of maxseqle = 37000, however, the output each time gives duplicated length around 75000 charcters per each sequence.
  clustalo.exe -i Allseq.fasta --is-profile --use-kimura --seqtype DNA --maxseqlen 37000 --threads 8 -o myclustalv3.fasta
  
  How can I solve this problem, what will I define in input parameters. This problem occurs with large no of sequences 600 sequences. In test of 40 seq, it gave me normal output length around 32000 characters but when align all 600 sequences together, it gave this duplicated length results.
  
  user4401: Have you had a look at your alignment? I personally use Jalview but any alignment viewer should work. Colour > Percentage Identity (or Nucleotide) should help with visualization.
  Does the alignment look reasonable (and gaps are just inserted at the end for some reason), or is it pretty messy? If it looks messy, is it just a few outlier sequences that cause the problem, or does it look like you have two main groups of sequences that align between themselves but not with the other? In the latter case, could it be possible that some of your initial sequences were inputed in the reverse orientation? I'm not sure about the command line implementation of Clustal Omega, but I know that at least the versions I use don't automatically reverse-complement sequences to be aligned.
  
original_text: 14295: <p>I am performing  multiple sequence alignment using Clustal Omega for 600 RNA covid-sequences, i.e. cDNA on Genbank, with input characters around 30574 characters for each sequence.</p>
  <p>I am running it on windows cmd.
  I defined parameters in input of maxseqle = 37000, however, the output each time gives duplicated length around 75000 charcters per each sequence.</p>
  <pre><code>clustalo.exe -i Allseq.fasta --is-profile --use-kimura --seqtype DNA --maxseqlen 37000 --threads 8 -o myclustalv3.fasta
  </code></pre>
  <p>How can I solve this problem, what will I define in input parameters. This problem occurs with large no of sequences 600 sequences. In test of 40 seq, it gave me normal output length around 32000 characters but when align all 600 sequences together, it gave this duplicated length results.</p>
   4401: <p>Have you had a look at your alignment? I personally use Jalview but any alignment viewer should work. Colour &gt; Percentage Identity (or Nucleotide) should help with visualization.</p>
  <p>Does the alignment look reasonable (and gaps are just inserted at the end for some reason), or is it pretty messy? If it looks messy, is it just a few outlier sequences that cause the problem, or does it look like you have two main groups of sequences that align between themselves but not with the other? In the latter case, could it be possible that some of your initial sequences were inputed in the reverse orientation? I'm not sure about the command line implementation of Clustal Omega, but I know that at least the versions I use don't automatically reverse-complement sequences to be aligned.</p>
  