Skip to main content

Table 2 Influence of the phylogeny on the likelihood ratio test between the models of dependent and independent changes

From: Inferring Methionine Sulfoxidation and serine Phosphorylation crosstalk from Phylogenetic analyses

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
  1. 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