Reading BEAST2 nexus trees

This module reads nexus tree files that are created by BEAST2. The function read_nexus_trees() has options to make it compatible with trees that were generated by the BREATH package and read transmission trees.

pyccd.read_nexus._breath_label_nodes(tree)

Annotating the node names and blockcount values to an ete3.Tree. This only works if the nodes names follow the name convention from above. That is %Node-label/blockcount% which is extracted in replace_match() above.

Parameters:

tree – Tree that will get blockcount annotations from node names

pyccd.read_nexus.read_nexus_trees(file: str, breath_trees: bool = True, label_transm_history: bool = True) → list

Function to read a nexus file that contains transmission trees. This assumes that trees are generated by BREATH BEAST2 package. The necessary information is the blockcount for every node/edge. This function will fully label the transmission history onto the tree.

By setting breath_trees to false the transmission history labeling is also disabled.

Parameters:

• file – Input file

• breath_trees – If true, will assume that the trees have the blockcount annotated (default)

• label_transm_history – If true, will label transmission ancestry (default)

Returns:

list of transmission trees