physquirrel 1.0.3

package for reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks and sequence alignments

physquirrel

physquirrel is a Python package for phylogenetic network analysis, with a focus on reconstructing semi-directed phylogenetic level-1 networks from quarnets and/or sequence alignments. The package provides tools to build and visualize phylogenetic networks, leveraging the Squirrel algorithm for efficient network reconstruction.

List of important features

• $\delta$-heuristic to construct quarnets (4-leaf subnetworks) from a multiple sequence alignment (in .fasta or .nexus format)
• Squirrel algorithm to construct semi-directed phylogenetic level-1 networks from quarnets
• Basic visualization of networks
• Exporting phylogenetic trees and networks in eNewick format
• Methods to extract information from a network (e.g. its set of splits, its displayed quarnets)

Installation

If you have an up-to-date version of Python installed on your device, the standard package manager pip should come pre-installed. Then, you can install physquirrel from PyPI by simply using the following command in a terminal:

python -m pip install physquirrel

Example usage

Importing the package

To get started with physquirrel, open a Python shell and import the package with:

import physquirrel as psq

Creating a set of quarnets

Use the $\delta$-heuristic to create a dense set of tf-quarnets from a multiple sequence alignment as follows:

msa = psq.MSA('path/to/msa/file.fasta')
Q = msa.delta_heuristic()

Alternatively, the dense set of tf-quarnets can also be loaded directly from a .txt file as follows:

Q = psq.DenseQuarnetSet('path/to/quarnet/file.txt')

This method assumes that the .txt file contains one line per tf-quarnet. The quarnets need to be one of the following two types:

1. SQ: a b c d for a quarnet on leaves ${a,b,c,d}$ with a split $ab|cd$.
2. 4C: a b c d for a quarnet on leaves ${a,b,c,d}$ with a four-cycle $a,b,c,d$ and the leaf $a$ below the reticulation.

Reconstructing a network

To create a semi-directed network from the dense set of tf-quarnets, run the Squirrel algorithm:

N = Q.squirrel()

To view the semi-directed network and print its eNewick string (with an arbitrary rooting), run:

N.visualize()
eNewick = N.create_enewick()
print(eNewick)

For a complete overview of different methods and extra parameter options, please check the method descriptions in the source code of physquirrel.

Citation

If you use physquirrel, please cite the corresponding paper:

Squirrel: Reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks and sequence alignments by Niels Holtgrefe, Katharina T. Huber, Leo van Iersel, Mark Jones, Samuel Martin, and Vincent Moulton.