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MUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.

Parameters in GUI

ParameterDescriptionDefault value
ModeSelector of preset configurations, that give you the choice of optimizing accuracy, speed, or some compromise between the two. The default favors accuracy.MUSCLE default
Stable orderDo 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

Type: muscle

ParameterParameter in the GUIType
modeMode

numeric

Availables values are:

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

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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