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Task Name: = align-mafft
Multiple sequence ali= gnment with MAFFT.
MAFFT is used as an external tool= and must be installed on your system.
Parameters:
toolpath =E2=80=94 path to the MAFFT executable. By = default, the path specified in the Application = Settings is applied. [String, Optional, Default: =E2=80=9Cdefault= =E2=80=9D]
tmpdir =E2=80=94 directory for temporary files. [Str= ing, Optional]
in =E2=80=94 semicolon-separated list of input files= . [String, Required]
out =E2=80=94 output file. [String, Required]
format =E2=80=94 format of the output file. [String,= Required]
op =E2=80=94 penalty for opening a gap. [Number, Opt= ional]
ep =E2=80=94 penalty for extending a gap. [Number, O= ptional]
maxiterate =E2=80=94 maximum number of cycles of ite= rative refinement. [Number, Optional]
Example:
ugene al= ign-mafft --in=3DCOI.aln --out=3DCOI_aligned.aln=20