Skip to end of metadata
Go to start of metadata

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

 

Icon

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.

Parameters in GUI

ParameterDescriptionDefault value
OffsetWorks like gap extension penalty.0
Gap open penaltyGap open penalty.1.53
Max iterationMaximum number of iterative refinement.0
Tool path (default)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: mafft

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 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
  • No labels