Skip to main content

Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Table 8 Proteobacteria Tree Accuracy Analysis. The scaled Robinson-Foulds (RF) distances [40] of the trees produced from the Proteobacteria dataset using fixing a model used to build trees from each alignment. The values reported are the median and average distance computed by comparing every tree against every other tree. When the optimal set of models were used the median was 0.22 and the average was 0.34. Phyml [53] was used to build all trees.

From: Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Model Median RF Mean RF Model Median RF Mean RF
Blosum 0.23 0.35 JTT 0.23 0.34
Blosum+I 0.25 0.35 JTT+I 0.25 0.35
Blosum+G 0.25 0.35 JTT+G 0.25 0.35
Blosum+I+G 0.25 0.35 JTT+I+G 0.25 0.35
CPREV 0.24 0.35 MtREV 0.25 0.35
CPREV+I 0.25 0.35 MtREV+I 0.25 0.35
CPREV+G 0.25 0.35 MtREV+G 0.25 0.35
CPREV+I+G 0.25 0.35 MtREV+I+G 0.25 0.35
Dayhoff 0.2 0.34 WAG 0.21 0.34
Dayhoff+I 0.21 0.34 WAG+I 0.23 0.35
Dayhoff+G 0.22 0.34 WAG+G 0.25 0.35
Dayhoff+I+G 0.22 0.34 WAG+I+G 0.25 0.35