Methods description

Species tree inference method

01 - Inference of species tree when assignment specified by user

Phase 1: Identification of species tree nodes X,Y and C.

1. Clone species tree and gene trees, and from now on, work on the cloned copies.
2. Calculate the weight of each branch of the species tree as the reciprocal of the square root of its length.
3. Randomly select an internal (non-terminal) branch according to weight (higher weight, more probable), and name the node closer to the root (parent) as node X, and the other one node Y.
4. Find all nodes that are candidates to become node C. Such node must fulfill three properties:
   • It is not a descendant of node Y.
   • It is younger than Y.
   • Its parent is older than Y.
5. For each C candidate node p, compute its weight as the reciprocal of number of nodes on the shortest path between p and Y. Once all weights are computed, normalize them.
6. Randomly select node C from the candidates according to their weights (higher weight, more probably).
7. Find node Z, the lowest common ancestor of nodes C and Y.

Phase 2: Update gene trees using SPR

1. for each gene tree do the following: