Multiple sequence alignment tool by Florence Corpet

Research published using this software should cite:
"Multiple sequence alignment with hierarchical clustering"
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890

Help with Multalin


Sequences need to be in one of the following formats: MultAlin/Fasta, Genbank, Embl-Swissprotein.
Click here for examples

Paste in sequences


Optional Parameters


Graphical results:


Sequence input format:
Sequence output format:


Scoring method:


Symbol comparison table - gap opening default value - gap extension default value :

Gap penalties : (default: value from comparison table)

Gap penalty at opening:

Gap penalty at extension:

Gap penalty at extremities:


One iteration only:



Text options

Text size Text color
Background color

Sequence options

High consensus color Low consensus color
Neutral color

High consensus value: % (default: 90%)
Low consensus value*: % (default: 50%)
*Must be less than first value.

Presentation options

Output style
Maximum line length
Graduation step


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For more information, contact sacs at cgl.ucsf.edu