The program also performs analyses with the MPL (mean-path-length) method, as described in Britton, T., B. I am working trying to decipher two large phylogenies and I am wondering about how to estimate confidence.Fortunately, intermediate models employing relaxed molecular clocks have been described. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.These models open the gate to a new field of ‘‘relaxed phylogenetics.’’ Here we introduce a new approach to performing relaxed phylogenetic analysis. Despite their obvious utility, detailed species-level phylogenies are lacking for many groups, including several major mammalian lineages such as bats.We provide this phylogenetic hypothesis, and an analysis of divergence times, as tools for evolutionary and ecological studies that will be useful until more inclusive studies using multiple loci become available.
Compiled versions for the following platforms are available: Windows XP Mac OS X Linux 2.4.20-31.9 (Red Hat 9), glibc 2.3.2 Unix (Sparc) The source files and compilation instructions are found here. The program works instantaneously even for very large phylogenetic trees.
In the past I had estimated confidence using boostrap and posterior probability when doing bayesian phylogenetic inference.
Now I am following up on the work but the databases have grown immensely to 15000-30000 sequences.
The output also contains results from the MPL analysis described in Britton et al.
(2002), which can be of interest when there are no fossil datings or if the clock hypothesis is of interest (a clock test is performed at each node).