I. Input screen

Names of species/branches: species A, B, C, and D can be replaced by authentic names. Note: names should not contain spaces or commas inside (e.g., “gray wolf” must be written as “gray_wolf”).

Settings:

Algorithms: Reverse is the preferred algorithm. In the case of rapidly radiating species, the Stepwise algorithm might provide a better resolution.

Criterion (Selection of approximations): The Chi-square criterion allows getting estimations in a few seconds. However, Chi-square could lead to an incorrectly preferred polytomy at resolution boundary. The Empirical distribution processes via a bootstrapping-like procedure to calculate critical values for each comparison and give a better resolution. However, the process could require up to an hour.

Marker Input: For the four lineages A,B,C,D, ten different patterns of relationships (y11-y44) can be derived. The supportive number of verified diagnostic TEs of each pattern has to be inserted in the Marker Input field. For calculation, the minimum input is one marker.

File Upload: Alternatively, all data can be uploaded from a text or excel file corresponding to the following example