Tree | Ln(L) | Fitch score | Topology difference | Branch score | LRT |
p-Value |
|---|
eggNOG | −43,009 | 7499 | 0 | 0 | 15.9 | 0.0030 |
NJ | −43,677 | 7596 | 198 | 1.664 | 20.8 | 0.0003 |
MP | −60,127 | 7472 | 28 | 426.745 | 14.1 | 0.0070 |
ML | −37,544 | 7511 | 111 | 1.118 | 17.1 | 0.0020 |
- Besides the pre-computed tree from eggNOG, trees reconstructed using the methods of neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML), were used to test the hypothesis of correlated evolution between Ser-218 and Met-222. In addition to the LRT and its related p-value, the table shows the natural logarithm of the likelihood, Ln(L), and the Fitch score for each tree. The distance between each tree and that from eggNOG was assessed using either the metric proposed by [53] (topology difference) or the branch score proposed by [54]. The former, is defined as twice the number of internal branches that differ in their splits, while the latter is defined as the sum of squares of the differences between each branch’s length in both trees
