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  • Align with ClustalO Element
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Aligns multiple sequence alignments (MSAs) supplied with ClustalO.

Parameters in GUI

ParameterDescriptionDefault value
Number of iterationsNumber of (combined guide-tree/HMM) iterations.1
Number of guidetree iterationsMaximum number guidetree iterations.0
Number of HMM iterationsMaximum number of HMM iterations.0
Set auto optionsSet 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.

Temporary directoryDirectory to store temporary files.Default

Parameters in Workflow File

Type: ClustalO

ParameterParameter in the GUIType
num-iterationsNumber of iterations


max-guidetree-iterationsNumber of guidetree iterationsnumeric
max-hmm-iterationsNumber of HMM iterationsnumeric
set-autoSet auto optionsboolean
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


Slot In GUISlot in Workflow FileType

And 1 output port:

Name in GUI: ClustalO result MSA

Name in Workflow File: out-msa


Slot In GUISlot in Workflow FileType
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