We compare our approach with two state-of-the-art PPI extraction methods: a tree kernel-based method [ 20] and a hybrid method [ 6].
Each "strategy" for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup.
Phylogenetic analysis was performed using Neighbor-joining method and a tree of the MC receptors is presented in Figure 2 and Additional file 2. The topology of the trees was the same with or without out-group (data not shown).
As for the ligands, several methods were used to construct unrooted trees for the receptors, but unlike the ligand trees, there is no significant difference in the trees from the different methods used, and all methods yield a tree similar to that previously constructed [ 1].
Figure 2 shows a phylogenetic tree obtained by the neighbor-joining method (a phylogenetic tree obtained by the maximum-likelihood method is shown in Supplementary Fig. S2).
Using a classical phylogenetic method, a gene tree, representing the evolution of the gene family by local mutations, can then be constructed based on the similarity scores.
Another difference is that logistic regression can be used to derive odds ratios for the significant risk factors, whereas tree-based methods create a tree where the ramifications represent the risk factors.
Using the same method, an unrooted tree was also obtained with the concatenated sequences from all 896 core Neisseria genes.
The values below 0.05 are in bold The third method was a tree-scanning analysis of associations between haplotypes and leaf parameters.
