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Parameters in GUI

Parameter	Description	Default value
Number of iterations	Number of (combined guide-tree/HMM) iterations.	1
Number of guidetree iterations	Maximum number guidetree iterations.	0
Number of HMM iterations	Maximum number of HMM iterations.	0
Set auto options	Set options automatically (might overwrite some of your options).	False
Tool path	Path to the ClustalO tool. The default path can be set in the UGENE application settings.	Default
Temporary directory	Directory to store temporary files.	Default

Schema File

Type: ClustalO

Parameter	Parameter in the GUI	Type
num-iterations	Number of iterations	numeric
max-guidetree-iterations	Number of guidetree iterations	numeric
max-hmm-iterations	Number of HMM iterations	numeric
set-auto	Set auto options	boolean
path	Tool path	string
temp-dir	Temporary directory	string

The element has 1 input port:

Name in GUI: Input MSA

Name in Schema File Workflow File: in-msa

Slots:

Slot In GUI	Slot in Schema Workflow File	Type
MSA	msa	malignment

And 1 output port:

Name in GUI: ClustalO result MSA

Name in Schema File Workflow File: out-msa

Slots:

Slot In GUI	Slot in Schema File	Type
MSA	msa	malignment