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  • Align with ClustalW Element

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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 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 main UGENE User Manual.

Parameters in GUI


ParameterDescriptionDefault value
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.default
End gapsThe penalty for closing a gap.False
Gap distanceThe gap separation penalty. Tries to decrease the chances of gaps being too close to each other.4.42
Gap extension penaltyThe penalty for extending a gap.8.52
Gap open penaltyThe penalty for opening a gap.53.90
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.False
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.False
Iteration typeAlignment improvement iteration type.None
Number of iterationsThe maximum number of iterations to perform.3
Tool path (required)Path to the ClustalW tool. The default path can be set in the UGENE Application Settings.default
Temporary directoryDirectory to store temporary files.default

Parameters in Workflow File

Type: clustalw

ParameterParameter in the GUIType
matrixWeight matrix


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
close-gap-penaltyEnd gapsboolean
gap-distanceGap distancenumeric
gap-ext-penaltyGap extension penaltynumeric
gap-open-penaltyGap open penaltynumeric
no-hydrophilic-gapsHydrophilic gaps offboolean
no-residue-specific-gapsResidue-specific gaps offboolean
iteration-typeIteration type


Available values are:

  • 0 - for None
  • 1 - for Tree
  • 2 - for Alignment
iterations-max-numNumber of iterationsnumeric
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: ClustalW result MSA

Name in Workflow File: out-msa


Slot In GUISlot in Workflow FileType