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Table 8 Results for tree inference on alignments generated using different methods, on the simulated datasets, as shown in Figure 15

From: Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs

 

Low

Medium

High

 
 

AMA

RF

AMA

RF

AMA

RF

 

MinRisk (C +), g=0

0.84

0.12

0.67

0.12

0.59

0.44

 

MinRisk (C), g=0

0.83

0.20

0.64

0.28

0.53

0.44

 

MAFFT

0.81

0.16

0.60

0.44

0.50

0.64

 

MUSCLE

0.80

0.36

0.61

0.48

0.49

0.48

 

T-Coffee

0.67

1.00

0.52

0.92

0.42

1.24

 

CLUSTALW2

0.62

1.04

0.44

1.32

0.35

1.36

 
  1. Shown are alignment accuracy scores (according to the AMA metric), and Robinson-Foulds tree distances (RF) for the DNAML tree, averaged over all datasets in each group (low, medium and high indel rates). Higher alignment accuracy is strongly predictive of tree accuracy, with the most accurate alignments generating the trees with the fewest errors (shown in bold). The MinRisk results were computed using samples generated by StatAlign.
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BMC Bioinformatics

ISSN: 1471-2105

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