Fast NJ-like algorithms to deal with incomplete distance matrices

BMC Bioinformatics

Table 3 Topological accuracy with datasets generated from Driskell et al. [20]

(a): Medium-level combination of the distance matrices being directly estimated from the gene sequences. (b): High-level 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 path-length distance matrices which are combined into the distance supermatrix. All combinations of source distance matrices are achieved using SDM. p-value: sign-test significance when comparing the 100 d_qvalues of MVR* (our best algorithm) to those of FITCH and MRP. For other symbols and notation, see note to Table 1.

ISSN: 1471-2105