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Originally, MAFFT is a multiple sequence alignment program for unix-like operating systems. Currently, Windows version is also available.


MAFFT 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.

MAFFT 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: mafft

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
OffsetWorks like gap extension penalty.0gap-ext-penaltynumeric
Gap open penaltyGap open penalty.1.53gap-open-penaltynumeric
Max iterationMaximum number of iterative refinement.0iterations-max-numnumeric
Tool path (default)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

Slots:

Slot In GUISlot in Workflow FileType
MSAmsamsa

And 1 output port:

Name in GUI: Multiple sequence alignment

Name in Workflow File: out-msa

Slots:

Slot In GUISlot in Workflow FileType
MSAmsamsa
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