parat estimates site specific substitution rates from a set of DNA
sequences. The rates and the phylogenetic tree relating the sequences
are estimated in an iterative maximum likelihood procedure, whereby
the likelihood of the inferred tree increases at each iteration step
until it converges.
Rates can be estimated from data sets containing up to 100 sequences
in one iteration procedure. For the analysis of datasets larger than
100 sequences, a subsampling procedure is implemented in parat. Here,
random subsamples are drawn from the sequence set, rates are estimated
from the subsamples with the iterative procedure and finally the
rate estimates are averaged.
The method is described in detail in the following article:
If you are using Parat, please cite this article.