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 |