(a): medium level


FITCH

MW*

NJ*

BIONJ*

MVR*
 
p value


     
MVR* – FITCH

MVR* – BIONJ*


0.0234

0.0268

0.0289

0.0227

0.0171
 
≈ 0.0

≈ 0.0

(b): high level

FITCH

MW*

NJ*

BIONJ*

MVR*

MRP

p
value

     
MVR* – FITCH

MVR* – MRP

0.0161

0.0165

0.0182

0.0172

0.0101

0.0119

0.001

0.193

 (a): Mediumlevel combination of the distance matrices being directly estimated from the gene sequences. (b): Highlevel combination; ML trees are first inferred separately for every genes; MRP turns the gene trees into a matrix of partial binary characters, which is analyzed with parsimony; with the other (distance) methods, the gene trees are turned into pathlength distance matrices which are combined into the distance supermatrix. All combinations of source distance matrices are achieved using SDM. pvalue: signtest significance when comparing the 100 d_{
q
}values of MVR* (our best algorithm) to those of FITCH and MRP. For other symbols and notation, see note to Table 1.