I. Input screen

Names of species/branches: species A, B, C, and D can be replaced by real names.

Significance Level: 0.05 for 95% can be replaced, e.g., by 0.01 for 99% significance level.

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

Marker Input: For four lineages 10 different patterns of relationships can be derived. The supportive number of TEs of each of these patterns has to be inserted in the Marker Input field. 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:

With Start hamlet calculation the process is commenced. With Reset user can return all values and settings to initial/default values.

II. Results screen

Example:

Names of species/branches: human, chimpanzee, gorilla and orangutan

Significance Level: 0.05

Algorithm: Reverse

Marker Input: 0 0 0 0 0 0 1 0 37 48

The resulting “Essential tree topology” is indicated as T2 for the exemplified data and the significance of the tree is placed as text below the tree topology. KKSC values for individual splits of the tree are given in the grey part. The log-likelihood table (LL-table) can be downloaded and provides information of optimal parameters for all five models. With Download LL table one can retrieve the results table of best trees from all five groups for further investigations.

“Model” indicating the tested model. “Alias” describing models in “TTgg” annotation, “Order” provide information about the permutation (where 1234 is equivalent to A,B,C,D); “LL” is presenting the log-likelihood value for the resulting trees, “Ratio” present the value of the double log-likelihood ratio between resulting tree and polytomy (reflecting χ2 value); “T(1)” and “T(3)” provide the relative length of tree branches (T1 and T3) that is proportionally to the number of generations on corresponding branches); γ(1) and γ(3) providing values of the hybridization coefficients (γ1 and γ3).

III. Extended system for tree notation in text format

  1. Round brackets “( )” indicate clustering groups: e.g. (A(B,C)) shows clustering of B and C against the sister-group A.
  2. Square brackets “[ ]” indicate hybridization of two external branches: e.g. (A[B]C) show hybridization/introgression between A and C resulting in branch B.
  3. Plus “+” indicating a common branch: e.g. (A(B,C+D)) shows a close relation of B to a common branch of C and D (later split into two branches).
  4. Vertical slash “|” indicating an ancestral hybridization situation, e.g. hybridization (A[C+D]B) following situation when C plus D have two sister-groups (A|B(C,D).
  5. Comma “,” indicates a shared origin, e.g. in the tree (A(B,C)) comma shows that B and C share the same origin, and in the tree (A,B,(C,D)) first two commas announce polytomy with shared origin of A, B and the common ancestor of C plus D.