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Table 2 Quality of the gene trees ( G NNI ) and reconciliations ( R NNI ) inferred by MowgliNNI on very short sequences

From: Reconciliation and local gene tree rearrangement can be of mutual profit

Threshold

20

80

95

Number of gene families containing weak edges

794

1000

1000

%cases s.t. C o s t ( S , G N N I ) < C o s t ( S , G M L )

89

97

97

%cases s.t. R F ( G T r u e , G N N I ) < R F ( G T r u e , G M L )

58

77

75

%cases s.t. R F ( G T r u e , G N N I ) = R F ( G T r u e , G M L )

39

16

16

%cases s.t. R F ( G T r u e , G N N I ) > R F ( G T r u e , G M L )

3

7

9

%cases s.t. E D ( R T r u e , R N N I ) < E D ( R T r u e , R M L )

78

91

91

%cases s.t. E D ( R T r u e , R N N I ) = E D ( R T r u e , R M L )

15

5

5

%cases s.t. E D ( R T r u e , R N N I ) > E D ( R T r u e , R M L )

7

4

4

  1. For each tested threshold value, the second row indicates the number of gene families (G ML ) containing some weak edges among 1000 families inferred from very short sequences of length 400 bp. Third row indicates the percentage of these families where MowgliNNI proposes a modified tree of lower reconciliation cost. The last six rows provide the percentage of the former families where MowgliNNI provides modified gene trees (resp. reconciliations) that are closer, equally far or farther from the true gene trees (resp. the true evolutions). RF(G True ,G X ) denotes the Robinson Foulds distance between G True  and G X , ED(R True ,R X ) = |R True  - R X | + |R X  - R True |, where X stands for NNI or ML.
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Algorithms for Molecular Biology

ISSN: 1748-7188