Generating Species Trees - thekswenson/Zombi_wiki GitHub Wiki

Basic Mode (T)

Zombi uses a Birth-death model to generate a species tree. Lineages can speciate given rise to two new lineages or go extinct over time. The usage is:

python3 Zombi.py T ./Parameters/SpeciesTreeParameters.tsv ./Output_folder

Once the Complete Species Tree is computed (CST), the extinct lineages are pruned so that the user can have the Extant Species Tree (EST). In real life, 99% of times we are interested in the EST, simply because the CST is mostly lost. However, if transfer events or introgressions have taken place along the branches of the trees, fragments of genomes from extinct lineages can have played a role in the evolution of the lineages present in the EST.

Output

CompleteTree.nwk The CST including the dead lineages, in newick format

ExtantTree.nwk The EST, in newick format

Events.tsv: Events (speciation and extinction) taking place in the species tree, along with the time they occur

CollapsedNodes.tsv: The second column gives the nodes of the CST that have been collapsed to create the resulting node in the EST, in the first column. You will rarely use this

Lengths.tsv

A file containing the length of the tree from the initial position to the leaves, the root, the stem and the crown (see below)

Parameters

SPECIATION, EXTINCTION

Rates of evolution for the different events

STOPPING_RULE

• 0: Time stops arriving at TOTAL_TIME
• 1: Tree evolves until a total of species = N_LINEAGES (alive) have been generated

TOTAL_TIME

To use with the stopping rule 0. Otherwise is ignored

N_LINEAGES

To use in combination with the stopping rule 1. Otherwise is ignored

MIN_LINEAGES

When using with the stopping rule 0, if the alive lineages in the tree are <= MIN_LINEAGES the run will be considered a failure and the program will start again

MAX_LINEAGES

If the run attains this number of lineage the simulation is killed ant the program will start again

VERBOSE

0 not to print the progress, 1 to do it