Task Name: align-mafft
Multiple sequence alignment with MAFFT.
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MAFFT is used as an external tool and must be installed on your system. |
Parameters:
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]
Example:
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ugene align-mafft --in=COI.aln --out=COI_aligned.aln |