Aligning with MAFFT

Task Name: align-mafft

Perform multiple sequence alignment using MAFFT.

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

Parameters:

  • toolpath — The path to the MAFFT executable. By default, the path specified in the Application Settings is used. [String, Optional, Default: “default”]

  • tmpdir — The directory for temporary files. [String, Optional]

  • in — A semicolon-separated list of input files. [String, Required]

  • out — The output file. [String, Required]

  • format — The format of the output file. [String, Required]

  • op — The penalty for opening a gap. [Number, Optional]

  • ep — The penalty for extending a gap. [Number, Optional]

  • maxiterate — The maximum number of cycles of iterative refinement. [Number, Optional]

Example:

ugene align-mafft --in=COI.aln --out=COI_aligned.aln
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