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T-Coffee is a multiple sequence alignment package.

T-Coffee home page: T-Coffee

To make T-Coffee available from UGENE see the External Tools.

To use T-Coffee open a multiple sequence alignment file and select the Align with T-Coffee item in the context menu or in the Actions main menu. The following dialog appears:

The following parameters are available:

Gap opening penalty — indicates the penalty applied for opening a gap. The penalty must be negative.

Gap extension penalty — indicates the penalty applied for extending a gap.

Number of iterations — specifies the number of iterations.

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