ClustalW

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Version

2.1 (Latest version)
1.83 (Modified by Dr. Kirill Kryukov)

Sequences

DNA Protein sequences
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Pairwise Alignment Parameters

Alignment Type:
Slow Fast

• Slow Pairwise Alignment Options

  • Protein Weight Matrix
    BLOSUM PAM Gonnet ID
  • DNA Weight Matrix
    IUB ClustalW
  • GAP OPEN
    100 50 25 10 5 2 1
  • GAP EXTENSION
    0.05 0.1 0.5 1.0 2.5 5.0 7.5 10.0

  Fast Pairwise Alignment Options

  • KTUP (WORD SIZE)
  • WINDOW LENGTH
    10 9 8 7 6 5 4 3 2 1 0
  • SCORE TYPE
    percent absolute
  • TOPDIAG
    10 9 8 7 6 5 4 3 2 1
  • PAIRGAP
    1 2 3 4 5 10 25 50 100 250 500

Multiple Sequence Alignment Parameters

• Protein Weight Matrix
  BLOSUM PAM Gonnet ID
• DNA Weight Matrix
  IUB ClustalW
• GAP OPEN
  100 50 25 10 5 2 1
• GAP EXTENSION
  0.05 0.20 0.5 1.0 2.5 5.0 7.5 10.0
• GAP DISTANCES
  10 9 8 7 6 5 4 3 2 1
• NO END GAPS
  no yes
• ITERATION
  none tree alignment
• NUMITER
  1 2 3 4 5 6 7 8 9 10
• CLUSTERING
  NJ UPGMA

• OUTPUT Options

  • FORMAT
  • ORDER
    aligned input
  • DOTSINOUTPUT (DDBJ original)
    off on