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. |
