Aligning with ClustalO

Task Name: align-clustalo

Create an alignment with ClustalO. ClustalO is a general-purpose multiple sequence alignment program for proteins.

ClustalO is used as an external tool and must be installed on your system.

Parameters:

  • in: Input alignment [URL datasets]

  • format: Document format of the output alignment (using ‘clustal’ by default) [String]

  • out: Output alignment [String]

  • max-guidetree-iterations: Maximum number of guide tree iterations (using ‘0’ by default) [Number]

  • max-hmm-iterations: Maximum number of HMM iterations (using ‘0’ by default) [Number]

  • iter: Number of (combined guide-tree/HMM) iterations (using ‘1’ by default) [Number]

  • toolpath: ClustalO location (using the path specified in UGENE by default) [String]

  • auto: Set options automatically (might overwrite some of your options) (using ‘False’ by default) [Boolean]

  • tmpdir: Directory to store temporary files (using UGENE temporary directory by default) [String]

Example:

ugene align-clustalw --in=test.aln --out=test_out.aln --format=clustal

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