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Comment: Migrated to Confluence 5.3

Task Name: pwm-build

Builds a position weight matrix from a multiple sequence alignment file.


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

out — output file. [String, Required]

type — type of the matrix. [Boolean, Optional, Default: false]

The following values are available:

    • true (dinucleic type)
    • false (mononucleic type)

Dinucleic matrices are more detailed, while mononucleic ones are more useful for small input data sets.

algo — algorithm used to build the matrix. [String, Optional, Default: “Berg and von Hippel”]

The following values are available:

    • Berg and von Hippel
    • Log-odds
    • Match
    • NLG


Code Block
ugene pwm-build --in=COI.aln --out=result.pwm