Unipro UGENE User Manual v. 38
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Aligns multiple sequence alignments (MSAs) supplied with ClustalW.

ClustalW is a general-purpose multiple sequence alignment program for DNA or proteins. Visit http://www.clustal.org/ to learn more about it.

Clustal 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 the main UGENE User Manual.

Element type: clustalw

Parameters


ParameterDescriptionDefault valueParameter in Workflow FileType
Weight matrixFor proteins, it is a scoring table which describes the similarity of each amino acid to each other. For DNA it is the scores assigned to matches and mismatches.defaultmatrix

numeric

Available values are:

  • 0 - for IUB
  • 1 - for ClustalW
  • 2 - for BLOSUM
  • 3 - for PAM
  • 4 - for GONNET
  • 5 - for ID
  • -1 - for default matrix
End gapsThe penalty for closing a gap.Falseclose-gap-penaltyboolean
Gap distanceThe gap separation penalty. Tries to decrease the chances of gaps being too close to each other.4.42gap-distancenumeric
Gap extension penaltyThe penalty for extending a gap.8.52gap-ext-penaltynumeric
Gap open penaltyThe penalty for opening a gap.53.90gap-open-penaltynumeric
Hydrophilic gaps offHydrophilic gap penalties are used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids.Falseno-hydrophilic-gapsboolean
Residue-specific gaps offResidue-specific penalties are amino specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment.Falseno-residue-specific-gapsboolean
Iteration typeAlignment improvement iteration type.Noneiteration-type

numeric

Available values are:

  • 0 - for None
  • 1 - for Tree
  • 2 - for Alignment
Number of iterationsThe maximum number of iterations to perform.3iterations-max-numnumeric
Tool path (required)Path to the ClustalW tool. The default path can be set in the UGENE Application Settings.defaultpathstring
Temporary directoryDirectory to store temporary files.defaulttemp-dirstring

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: ClustalW result MSA

Name in Workflow File: out-msa

Slots:

Slot In GUISlot in Workflow FileType
MSAmsamsa



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