For epiphytic lichens, sampling follows a standard procedure for tree selection after stratification by bark type.
We suppose that this method can be utilized as a standard procedure for tree comparisons.
Let in this procedure a tree G′ be already derived and possess a polytomous vertex g.
As a result of this procedure, a tree of orthologous groups was obtained.
Phylogenetic analyses for each of the 7 genes that include the putative paralogs found by this procedure produced tree topologies that strongly suggest an ancient duplication event in the vertebrate lineage, before the divergence of tetrapods from ray-finned fishes.
These HGT-genes-filtrated genomes were subjected to our tree-construction procedure and produced Tree HGT- (Additional file 2b).
The procedure "trace over trees" was used to summarize reconstructions over 1000 randomly sampled BEAST trees (after the burn-in).
The procedure produces tree-like rule structures that predict outcomes.
As mentioned below, the procedure of trees simulation along a topology needs further study and justification.
In this procedure, 10 000 trees were grown and 5 among the 241 parameters were used at each node.
We used the same procedures for tree reconstruction as described above for the 13 mt protein-coding genes.
