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	Sequence Data Expression Data Images Documents More... Tools Get Data Search User BLAST ClustalW HMMER
	ClustalW @ VectorBase.org: New Multiple Alignment » Directions: Paste or upload sequences. Select protein or dna sequences. Optional: Set additional ClustalW parameters. Submit your ClustalW job. Sequence Type: Sequence Type: protein dna ClustalW Options:  Parameters: Default [More options]  Alignment: full fast kTuple (Word Size): default 1 2 3 4 5 Window Length: default 10 9 8 7 6 5 4 3 2 1 0 Score Type: percent absolute Top Diagonals: default 10 9 8 7 6 5 4 3 2 1 Gap Penalty: default 1 2 3 4 5 10 25 50 100 250 500 Matrix: GONNET (protein) BLOSUM (protein) PAM (protein) Identity (both) IUB (dna) Open Gap Penalty: default 1 2 5 10 25 50 100 End Gap Penalty: default 10 20 Gap Extension Penalty: default 0.05 0.5 1.0 2.5 5.0 7.5 10.0 Gap Separation Penalty: default 10 9 8 7 6 5 4 3 2 1 Output Format: aln gcg MSF phylip pir gde nexus Output Order: aligned input Input Sequences (100Kb / 100 Sequence Limit):  Upload a file:  OR  Paste in sequences in FASTA format: Job Control:  Submit your ClustalW job  Retrieve a previously run ClustalW job   •
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