Methods
The MCMC simulations were run with
BAMBE as follows:
-
100,000 Metropolis-Hastings steps for the burn-in phase,
using global tree re-arrangements.
-
100,000 Metropolis-Hastings steps for the sampling phase,
using local re-arrangements and storing trees every
200 Metropolis-Hastings steps.
For further details, see the
BAMBE inputfile.
In all other respects,
the methods were applied as described in
Bioinformatics 17, S123-S131.
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