Input tree (Ti)

This mode allows the user to input a species tree. In this case, the command is slightly different:

python3 Zombi.py Ti YourTreeFileInNewick ./Output_folder

This command will translate your tree into a file with the events taken place on it, something used by the other modes of Zombi. If you want to simulate genomes in your own tree, running this command is a prerequisite.

Some caveats when using this mode:

Zombi assumes that the tree you use as input is the Complete Species Tree. This means that all living lineages have the same distance from the leaves to the root and dead lineages are shorter branches that do not arrive until the present time.

Zombi does not support multifurcation.

Zombi does not support trees with 0 branch-length either.