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Basic query

General options
Alignment title		Your E-Mail
Alignment Slow Fast	Show dendrogram Off On	Output format CLUSTAL GCG PHYLIP PIR GDE	Output order Aligned Input

Fast pairwise alignment options
K-Tuple (Word size) 1 2 3 4	Window length	TOPDIAG	PAIRGAP	Score type Percent Absolute

Slow pairwise alignment options
Protein weight matrix BLOSUM PAM GONNET ID	DNA weight matrix IUB CLUSTALW	Gap open	Gap extension

Multiple alignment options
Type Auto DNA Protein	Protein weight matrix BLOSUM PAM GONNET ID	DNA weight matrix IUB CLUSTALW	Gap open	Gap extension

Phylogenetic tree			Other advanced ClustalW 1.83 options for experts
Tree type none nj phylip dist	Kimura's correction Off On	Ignore gaps Off On
Picture Options
Picture width	Picture height	Picture formats None Slanted Slanted 2 Rectangular Rectangular 2 Phylogram Unrooted Unrooted 2	Max/min factor for Unrooted 2

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Last updated: May 22, 2001.