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  • Align with T-Coffee Element

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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.

Parameters in GUI

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

Parameters in Workflow File

Type: tcoffee

ParameterParameter in the GUIType
gap-open-penaltyGap open penaltynumeric
iterations-max-numMax iterationnumeric
pathTool pathstring
temp-dirTemporary directorystring

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