Multiple Alignment Tools

1. ClustalW

  ClustalW is a multiple sequence alignment tool.

• Input formats: FASTA, NBRF/PIR, EMBL/SwissProt, GDE, Clustal, GCG/MSF, RSF.  Remove any white space space or empty lines from the beginning of your input.
• Results: you may choose between email (default) and interactive runs.
• Alignment: you may choose to run a full alignment or using a stringent algorithm for generating the tree guide or a fast algorithm.
• Output: options of output are are ALN, GCG, PHYLIP, PIR and GDE. You may have color alignments.

  Types of Alignments:

  Fast Pairwise Alignment Options

  • KTUP: allows you to choose a 'word length'
  • WINDOW: you may set the window length
  • SCORE: allows you to specify a score threshold
    PAIRGAP: you may set the gap penalty

  Multiple Sequence Alignment Options

  • MATRIX: allows you to choose which matrix series to use
    1. BLOSUM  (appear to be the best available for carrying out homology searches)). BLOSUM80, 62, 40 and 30 matrices are used.
    2. PAM: extremely widely used, PAM 120,160, 250 and 350 matrices.
  • GAPOPEN: you can set here the penalty for opening a gap
  • ENDGAP: you can set here the penalty for closing a gap
  • GAPEXT: you can set here the penalty for extending a gap.
  • GAPDIST: you can set here the gap separation penalty

Click here for more information on ClustalW  

2.Multalign

Multalign is also a  multiple sequence alignment tool.  The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix  that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the  process can be performed. These are the following two version of Multialign.

Multalign for Protein Sequence Alignment
Multalign for DNA Sequence Alignment
 

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