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.

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


Keane et al. BMC Evolutionary Biology 2006 6:29   doi:10.1186/1471-2148-6-29

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