Empty values or values that start with a ? are treated as missing values. Depending on the Distance Calculation Settings these missing values are either treated as an own category or ignored during pairwise comparison.

For a lower number of columns for distance calculation, (e.g. for MLVA data or MLST data), the missing values are an own category option is recommended. For a larger number of columns (e.g. MLST with hundreds of targets) the pairwise ignore missing values option is recommended.

Note that the option pairwise ignore missing values may result in problems in the tree when a Sample contains many missing values. It is recommended to remove Samples that have missing values in more than 10% of the columns for distance calculation before calculating a tree.