Child pages
  • Aligning with MAFFT

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migrated to Confluence 5.3

Task Name: align-mafft

Multiple sequence alignment with MAFFT.

Warning

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:

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