plot_toads.m.
The graph below was obtained from a sequence alignment
of four nematodes. This clearly indicates a recombination event at the
beginning of the alignment, corresponding to a transition from
topology 3 into
topology 2.
Note, however, that by discarding all but the topology-defining
sites you lose a substantial amount of information.
For example, the DNA sequence alignment used for
the analysis
below is 1567 bases long, but contains only
37 topology-defining sites.
Also, note that in certain situations
a classification based on topology-defining sites
can give the wrong answer - this is the well-known
problem of long-branch attraction, where parsimony
is known to fail.
TOADS should therefore only be applied as a
quick preliminary scan
of the data to be followed up by a proper
likelihood-based phylogenetic method like
BARCE.
However, the initialization of BARCE can profit
substantially from a preliminary scan of the
alignment with TOADS.
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Last modified: August 2003