| If -cons_truncate is specified, terminal gaps are counted for creating consensus sequences. By default, terminal gaps are ignored. The effect of -cons_truncate is to remove columns at the right-hand end of the alignment where gaps are most common, i.e. to truncate. This option should be used in cases where input sequences are full-length. By default, it is assumed that terminal gaps represent incomplete sequences (e.g., quality trimmed reads), in which case terminal gaps do not represent biological deletions. |