Extract Consensus as Text

For each input multiple alignment, the workflow calculates the consensus and saves it to a plain text file, named according to the input alignment name.

By default, the JalView algorithm (denoted as “default”) is used to calculate the consensus. For each alignment column:

• If two characters have high frequency, a "+" symbol is inserted.
• Otherwise, a character is returned either in uppercase or lowercase, depending on the percentage value and the threshold parameter.

Alternatively, you can choose the ClustalW algorithm:

• "*" — all characters in the column are identical.
• ":" — conserved between strongly similar properties (score > 0.5 in the Gonnet PAM 250 matrix).
• "." — conserved between weakly similar properties (score < 0.5).
• " " — no conservation.

Note: The threshold parameter does not apply to the ClustalW algorithm.

How to Use This Sample

If you haven’t used the workflow samples in UGENE before, see How to Use Sample Workflows.

Workflow Sample Location

This sample, “Extract Consensus as Text”, can be found in the “Alignment” section of the Workflow Designer samples.

Workflow Image

The opened workflow looks as follows:

Workflow Wizard

The wizard includes 3 pages:

1. Input Multiple Alignments

On this page, you must input multiple alignment file(s).

2. Extracting Consensus Settings

Modify the consensus extraction parameters here.

3. Output Files

Each input alignment produces a corresponding text file with the consensus string.