Task Name: pwm-build
Builds a position weight matrix from a multiple sequence alignment file.
Parameters:
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
Example:
| Code Block |
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ugene pwm-build --in=COI.aln --out=result.pwm |