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  • Aligning with MUSCLE
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Task Name: align

Performs multiple sequence alignment with MUSCLE algorithm and saves the resulting alignment to file. Source data can be of any format containing sequences or alignments.


in - Input alignment [Url datasets]
max-iterations -
Maximum number of iterations (using '2' by default) [Number]
mode -
Selector of preset configurations, that give you the choice of optimizing accuracy, speed,or some compromise between the two. The default favors accuracy (using 'MUSCLE default' by default) [Number]
range -
Whole alignment or column range e.g. 1..100 (using 'Whole alignment' by default) [String]
stable -
Do not rearrange aligned sequences (using 'True' by default) [Boolean]
format -
Document format of output alignment (using 'clustal' by default) [String]
out -
Output alignment [String]


ugene align  --in=test.aln --out=test_out.aln --format=clustal
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