ProfDistS

ProfDistS is a specialized application designed to assist users with the construction of large phylogenetic trees by relying on profile distances. It can be used via a modern graphical user interface and can display phylogenetic trees using a couple of third-party utilities.

ProfDistS provides users with a phylogenetic framework which uses individual RNA secondary structures for reconstructing phylogenies. It is based on sequence-structure alignments, and it uses Profile Neighbor Joining, with either manual or iterative and automatic profile definition. The application can also handle protein sequences.

Before anything else, you ought to make sure either TreeView or NJplot is installed on your PC. While the program can run without these utilities, they are required in order to display phylogenetic trees. You can configure their paths from the application’s settings.

ProfDistS can transform the imported alignments using three methods: profile neighbor joining, RNA bootstrapping and distance calculation. After loading the file, you can select the preferred method from the context menu.

When trying to view phylogenetic trees, the application will open them using the external application you have defined in the settings.

If you need assistance with any aspect of the software’s functionality, you can access the online documentation via the Help menu.