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  • Align with T-Coffee Element

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Warning

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 Schema File

Type: tcoffee

ParameterParameter in the GUIType
gap-ext-penaltyOffsetnumeric
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 Schema File: in-msa

Slots:

Slot In GUISlot in Schema FileType
MSAmsamsa
 

And 1 output port:

Name in GUI: Multiple sequence alignment

Name in Schema File: out-msa

Slots:

Slot In GUISlot in Schema FileType
MSAmsamsa