Multiple Sequence Alignment

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General Setting Parameters:

Output Format:

Pairwise Alignment: FAST/APPROXIMATE SLOW/ACCURATE

Enter your sequences (with labels) below (copy & paste): PROTEIN DNA

Support Formats: FASTA (Pearson), NBRF/PIR, EMBL/Swiss Prot, GDE, CLUSTAL, and GCG/MSF

Or give the file name containing your query

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Pairwise Alignment Parameters:

For FAST/APPROXIMATE:

K-tuple(word) size:, Window size:, Gap Penalty:
Number of Top Diagonals:, Scoring Method:

For SLOW/ACCURATE:

Gap Open Penalty:, Gap Extension Penalty:
Select Weight Matrix:

(Note that only parameters for the algorithm specified by the above "Pairwise Alignment" are valid.)

Multiple Alignment Parameters:

Gap Open Penalty:, Gap Extension Penalty:

Weight Transition:YES (Value: ), NO
Hydrophilic Residues for Proteins:
Hydrophilic Gaps:YESNO

Select Weight Matrix:

Type additional options (delimited by whitespaces) below:

(-options for help)

Multiple Sequence Alignment by CLUSTALW

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