Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria
Introduction: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.
Reference:The method is described in detail in the following article: