Clone this repo to your computer and use as you please

For using these scripts you will need to install the library ete3

pip install ete3

You might need also six (a dependency of ete3)

pip install six

• bootstrap_constraints.py

Bootstrap a file of transfers (read with parse transfers) and outputs a given number of replicates from those transfers, sampling with replacement

• count_orders.py

It tells you how many ranked trees there are for a given tree. Thanks to Sebastián Izquierdo (https://es.wikipedia.org/wiki/Sebasti%C3%A1n_Izquierdo) for his help

• compute_reds.py

Computes the RED tree

• get_constraints.py

Prints the constraints given a set of transfers and a species tree

• get_node_order.py

Reads a tree, outputs the node order of the tree. The format is, from the oldest to the youngest separated by commas

• get_agreement.py

Receives a constraints file and a node orders file and returns the agreement

• generate_orders.py

Generates all the possible ranked trees for a given tree. Watch out, for some trees the number of possibilities might be larger than the number of atoms in the universe.

• map_trees.py

Map the inner nodes of a reference tree to a set of trees

• mc_explorer.py

Explores ranked trees using a Bayesian approach. You can use it to generate a set of trees compatible with a set of constraints by setting a very low temperature

• parse_transfers.py

Reads all the uTs files in your current file and prints all transfers

• propagate_constraints.py

Takes a species tree, a calibration file (PhyloBayes format) and a constraint file (.tsv, see TestFiles for an example)

Returns the annotated species tree in which the inner nodes are called:

UPPERCONSTRAINT_LOWERCONSTRAINT

• read_bootstrap.py

Reads a set of files (output of MaxTiC, partial order) and it gives you the number of times that a constraint was found

• ultrametrice.py

Receives a tree and a node order (see script get_node_order.py) and outputs the ultrametric tree with that node order