Article,
Quartet-based phylogenetic inference: improvements and limits.
Mol Biol Evol, 18 (6): 1103--1116 (June 2001)
Abstract
We analyze the performance of quartet methods in phylogenetic reconstruction.
These methods first compute four-taxon trees (4-trees) and then use
a combinatorial algorithm to infer a phylogeny that respects the
inferred 4-trees as much as possible. Quartet puzzling (QP) is one
of the few methods able to take weighting of the 4-trees, which is
inferred by maximum likelihood, into account. QP seems to be widely
used. We present weight optimization (WO), a new algorithm which
is also based on weighted 4-trees. WO is faster and offers better
theoretical guarantees than QP. Moreover, computer simulations indicate
that the topological accuracy of WO is less dependent on the shape
of the correct tree. However, although the performance of WO is better
overall than that of QP, it is still less efficient than traditional
phylogenetic reconstruction approaches based on pairwise evolutionary
distances or maximum likelihood. This is likely related to long-branch
attraction, a phenomenon to which quartet methods are very sensitive,
and to inappropriate use of the initial results (weights) obtained
by maximum likelihood for every quartet.
