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Copyright © 2000, 2003 Malay Kumar Basu
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Program Name

clustalw

Output format

Pairwise Alignment Fast/approximate Slow/Accurate

Pairwise alignment parameters for fast/approximate

K-tuple(word) size

Window size

Gap Penalty

Number of Top Diagonals

Scoring Method

Pairwise alignment parameters for slow/accurate

Gap Open Penalty

Gap Extension Penalty

Weight Matrix

Multiple alignment parameters

Gap Open Penalty

Gap Extension Penalty

Weight Transition Yes No

Weight transition value

Hydrophilic Residues for Proteins

Hydrophilic Gaps Yes No

Weight Matrix

Additional options (delimited by whitespaces)

block maker  
Your email Sequence Description
ClustalW
At Kyoto university bioinformatics center. Align multiple sequence. Input type, DNA or protein sequences. See help to find out the input format of the sequences. Required option, none.
Block Maker
At Fred Hutchinson Cancer Research Center. Finds conserved blocks in a group of two or more unaligned protein sequences. At least two protein sequences must be provided to make blocks. Each sequence must have a unique name of 10 characters or less. All sequences must be of same format (FASTA). Input type- protein sequences. Required option- email for 25 sequences or more than 15,000 amino acids.