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Task Name: align-mafft

Multiple sequence alignment with MAFFT.


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


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

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

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

out — output file. [String, Required]

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

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

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

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


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