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 main UGENE User Manual.
Parameters in GUI
Parameter | Description | Default value |
---|---|---|
Weight matrix | For 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 gaps | The penalty for closing a gap. | False |
Gap distance | The gap separation penalty. Tries to decrease the chances of gaps being too close to each other. | 4.42 |
Gap extension penalty | The penalty for extending a gap. | 8.52 |
Gap open penalty | The penalty for opening a gap. | 53.90 |
Hydrophilic gaps off | Hydrophilic 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 off | Residue-specific penalties are amino specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment. | False |
Iteration type | Alignment improvement iteration type. | None |
Number of iterations | The 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 directory | Directory to store temporary files. | default |
Parameters in Workflow File
Type: clustalw
Parameter | Parameter in the GUI | Type |
---|---|---|
matrix | Weight matrix | numeric Available values are:
|
close-gap-penalty | End gaps | boolean |
gap-distance | Gap distance | numeric |
gap-ext-penalty | Gap extension penalty | numeric |
gap-open-penalty | Gap open penalty | numeric |
no-hydrophilic-gaps | Hydrophilic gaps off | boolean |
no-residue-specific-gaps | Residue-specific gaps off | boolean |
iteration-type | Iteration type | numeric Available values are:
|
iterations-max-num | Number of iterations | numeric |
path | Tool path | string |
temp-dir | Temporary directory | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input MSA
Name in Workflow File: in-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |
And 1 output port:
Name in GUI: ClustalW result MSA
Name in Workflow File: out-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |