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T-Coffee is a multiple sequence alignment package.

T-Coffee is used as an external tool from UGENE and it must be installed on your system. To learn more about the external tools, please, read main UGENE User Manual.

Element type: tcoffee


ParameterDescriptionDefault valueParameter in Workflow FileType
Gap extension penaltyGap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments.0gap-ext-penaltynumeric
Gap open penaltyGap open penalty. Must be negative, best matches get a score of 1000.-50gap-open-penaltynumeric
Max iterationNumber of iteration on the progressive alignment. 0 - no iteration, -1 - Nseq iterations.0iterations-max-numnumeric
Tool path (required)Path to the ClustalW tool. The default path can be set in the UGENE Application Settings.defaultpathstring
Temporary directoryDirectory to store temporary files.defaulttemp-dirstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input MSA

Name in Workflow File: in-msa


Slot In GUISlot in Workflow FileType

And 1 output port:

Name in GUI: Multiple sequence alignment

Name in Workflow File: out-msa


Slot In GUISlot in Workflow FileType
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