Documentation

Input Files

Three files are required as input: The host tree, the parasite (symbiont) tree, and a tip mapping.

The host and parasite trees must be in newick format and have the extensions .nwk. These trees can have branch length information, but eMPRess ignores it. However, species names should have no whitespace in them. The newick standard used here is that whitespace should be replaced with an underscore symbol. For example Diomedea epomophora should, instead, be Diomedea_epomophora.

The mapping is a text file that ends with the extension .mapping and specifies the association of the tips of the parasite tree to the tips of the host tree. Each line in the file is of the form:

parasiteTipName : hostTipName

Note that this mapping must associate each parasite tip with at most one host tip. It is fine for a parasite tip not to be mapped to any host tip, but a parasite tip cannot be mapped to more than one host tip. Similarly, it is fine for a host tip not to be mapped from any parasite tip. Finally, it's fine for multiple parasite tips to be mapped to the same host tip.

Running eMPRess through the Graphical User Interface

Documentation on running eMPRess through the GUI is available here.

Running eMPRess through the Command Line Interface

Documentation on running eMPRess through the Command Line Interface is available here.