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Parameters

Parameter	Description	Default value	Parameter in Workflow File	Type
Mode	Selector of preset configurations, that give you the choice of optimizing accuracy, speed, or some compromise between the two. The default favors accuracy.	MUSCLE default	mode	numeric Availables values are: 0 - for MUSCLE default 1 - for Large alignment 2 - for Refine only
Stable order	Do not rearrange aligned sequences (-stable switch of MUSCLE). Otherwise, MUSCLE re-arranges sequences so that similar sequences are adjacent in the output file. This makes the alignment easier to evaluate by eye.	True

Parameters in Workflow File

ParameterParameter in the GUITypemodeMode

numeric

Availables values are:

• 0 - for MUSCLE default
• 1 - for Large alignment
• 2 - for Refine only

Type: muscle

stable

Stable order

boolean

The element has 1 input port:

Name in GUI: Input MSA

Name in Workflow File: in-msa

Slots:

And 1 output port:

Name in GUI: Multiple sequence alignment

Name in Workflow File: out-msa

Slots: