Library for the Development and Use of Phylogenetic Network Methods
The Newick module provides utilities for handling Newick format strings and generating Nexus files from networks and gene trees.
Raised when there are errors parsing a Newick string into a Network object.
Extract all unique taxa labels from a Newick string.
| Parameter | Type | Description |
|---|---|---|
| newick_str | str | A Newick format string |
Class for generating Nexus files from tree/network data. Automatically manages taxa blocks and can include PhyloNet commands.
Initialize a blank Nexus template.
Add a network (as Newick string) to the TREES block. Taxa labels are automatically extracted and added to the TAXA block.
| Parameter | Type | Description |
|---|---|---|
| newick_str | str | Network in Newick format |
Add a PhyloNet command to be included in the PHYLONET block.
| Parameter | Type | Description |
|---|---|---|
| cmd | str | A PhyloNet command string |
Load gene trees from a file and add them to the template.
| Parameter | Type | Description |
|---|---|---|
| filename | str | Path to file containing gene trees |
Generate a Nexus file at the specified location.
| Parameter | Type | Description |
|---|---|---|
| loc | Path | str | Directory to save the file |
| end_name | str | Filename (must include .nex extension) |
NewickParserError - If file already exists
The NexusTemplate generates files with the following structure:
#NEXUS
BEGIN TAXA;
DIMENSIONS NTAX=n;
TAXALABELS
taxon1
taxon2
...
;
END;
BEGIN TREES;
Tree net1 = (newick_string1);
Tree net2 = (newick_string2);
...
END;
BEGIN PHYLONET;
command1;
command2;
...
END;from PhyNetPy.Newick import NexusTemplate, get_labels
# Extract labels from a Newick string
newick = "((A:1,B:1)C:1,(D:1,E:1)F:1)root;"
labels = get_labels(newick)
print(f"Taxa: {labels}") # {'A', 'B', 'C', 'D', 'E', 'F', 'root'}
# Create a Nexus file from networks
template = NexusTemplate()
# Add networks
template.add("((A:1,B:1):1,(C:1,D:1):1);")
template.add("((A:1,C:1):1,(B:1,D:1):1);")
# Add PhyloNet commands
template.add_phylonet_cmd("InferNetwork_MPL (all) 1;")
# Generate the file
template.generate("/path/to/output", "networks.nex")
# Load gene trees and create Nexus
template2 = NexusTemplate()
template2.load_gene_trees("gene_trees.nex")
template2.add_phylonet_cmd("InferNetwork_ML (all) 2 -bl;")
template2.generate("/path/to/output", "inference_input.nex")