MUSCLE
Enter or Paste a set of Sequences in any supported format.
All sequences must be in the same format :
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OR Upload Sequence file (upto 4.5 M)* : 





Parameters :


-maxiters     Maximum number of iterations(must be integer)


-diags    Find diagonals (faster for similar sequences)



HELP :


Maxiters




Top
You can control the number of iterations that MUSCLE does by specifying the –maxiters option. If you specify 1, 2 or 3, then this is exactly the number of iterations that will be performed. If the value is greater than 3, then muscle will continue up to the maximum you specify or until convergence is reached, which ever happens sooner. The default is 16. If you have a large number of sequences, refinement may be rather slow.


Diags




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The –diags option enables an optimization for speed by finding common words (6-mers in a compressed amino acid alphabet) between the two sequences as seeds for diagonals. This is related to optimizations in programs such as BLAST and FASTA: you get faster speed, but sometimes lower average accuracy. For large numbers of closely related sequences, this option works very well.