Example
muscle -addconfseq diversified_ensemble.efa -output with_confseqs.efaDescription
The addconfseq command adds two sequences of digits to each MSA replicates in an ensemble. The digits specify column confidence values to two decimal places. The sequence labels are _conf_ and _conf_2. In a given column, _conf_ is the first decimal place and _conf_2 is the second decimal place, so e.g. 73 means 0.73. A confidence of 1.0 is indicated as ++.
See also the letterconfs command which generates letter confidence values.
