cloak command

Example

Description

CLOAK generates a single filtered alignment from an alignment ensemble. If characters are found to be homologous across all alignments in the ensemble, they are retained in the filtered alignment. Otherwise they are replaced by dashes. If a whole alignment column does not have consistent homology, but subsets of the column do, the column is split into 2 or columns that are both retained in the filtered alignment.

-input_ensemble_file : Path to the input MSA file, which can either be an EFA file or a text file with paths to individual MSAs on each line

-mincol : Minimum number of non-gap characters required per column for that column to be retained in the output. Default value of 2 if not specified

-output : Name of the file where the filtered MSA will be written. By default this will be {input_file_name}.cloak.fa