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BayesPhylogenies is a specialized application designed to be used by biologists for inferring phylogenetic trees using two separate methods. It supports multiple models of gene sequence evolution, models for rooted trees and morphological traits, as well as gamma and beta distributed rate-heterogeneity.

The program uses a so-called “mixture model” that enables users to fit more than one sequence evolution model without having to partition the data.

The application itself is distributed in the form of an archive, and it does not need to be installed before use. Once unpacked, you can just run the executable file to get started.

It is worth noting that the program lacks a GUI, so it has to be used from the command-line. However, you don’t need to open Command Prompt manually, as the utility will be opened in the console automatically.

After launching the program, you will need to point it to the location of the Nexus file you wish to process. Once the file name has been provided, you can also enter various other parameters that affect the process in certain ways.

A detailed user manual is also included in the downloadable archive, and it is a good idea to consult it in order to find how you can make the most of this application.