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Table 1 Quality of the gene trees ( G NNI ) and reconciliations ( R NNI ) inferred by MowgliNNI depending on the length of the sequences used to obtain G ML trees and on the threshold indicating weak edges

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

  Short sequences Long sequences
Threshold 20 80 95 20 80 95
Number of gene families containing weak edges 163 323 327 118 328 332
%cases s.t. C o s t ( S , G N N I ) < C o s t ( S , G M L ) 80 92 91 75 83 84
%cases s.t. R F ( G T r u e , G N N I ) < R F ( G T r u e , G M L ) 43 74 73 29 67 67
%cases s.t. R F ( G T r u e , G N N I ) = R F ( G T r u e , G M L ) 53 17 18 67 26 24
%cases s.t. R F ( G T r u e , G N N I ) > R F ( G T r u e , G M L ) 4 9 9 4 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 ) 66 82 83 51 76 76
%cases s.t. E D ( R T r u e , R N N I ) = E D ( R T r u e , R M L ) 24 12 12 33 20 19
%cases s.t. E D ( R T r u e , R N N I ) > E D ( R T r u e , R M L ) 10 6 5 16 4 5
  1. Threshold of 20, 80 and 95 bootstrap support values are reported and sequence alignments of length in the range 1500 - 2000 bp (short seq.) or 2500–3000 bp (long seq.) were considered. For each threshold, the second row indicates the number of gene families (G ML ) containing weak edges among the 327 (resp. 336) families inferred from short (resp. long) sequences. The 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 reconciliations). 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.