Sequences should preferably be in FASTA format with each sequence separated by a line begining with a > sign

Please choose a nucleotide or protein sequence to align protein nucleotide

These are the basic options that you can set for clustalw:

Check this box for the quick and fast alignment. This is not recommended.

Output in CLUSTAL GDE GCG PHYLIP PIR format.

Output in   the input order.    the aligned order.

Include sequence numbers.    Do not include sequence numbers.

There are a large number of alternate parameters that you can set, and most of these are shown below. Note that if your selected nucleotide or protein for the alignments using the checkboxes above the default values will automatically change.

Clicking on the links will open the help page in a new window.

Pairwise Alignment Parameters:

For fast and approximate searches:
K-tuple(word) size
Window size
Gap Penalty
Number of Top Diagonals
Scoring Method	percent absolute
For slow and accurate searches:
Gap Open Penalty
Gap Extension Penalty
Weight Matrix	BLOSUM PAM GONNET ID

Multiple Alignment Parameters:

Gap Open Penalty
Gap Extension Penalty
Weight Transition	Yes: Value No
Hydrophilic Residues for Proteins
Hydrophilic Gaps	Yes No
Weight Matrix	BLOSUM PAM GONNET ID

Type additional options (-options for help)