Quickstart

This page shows the minimal steps to go from a sequence alignment to a phylogenetic network in physquirrel. For more details, see the Manual and the Installation page.

Install

pip install physquirrel

Run Squirrel

import physquirrel as psq

# Load a multiple sequence alignment (.fasta, .fa, .fas, .nexus, .nex)
msa = psq.MSA.load("alignment.fasta")

# Reconstruct a semi-directed level-1 network
network = psq.squirrel_from_msa(msa)

# Print the eNewick string
print(network.to_string())

# Save to file
network.save("network.nwk")

That is all that is needed. By default the network is unrooted (SemiDirectedPhyNetwork). To root it, pass an outgroup taxon name:

rooted = psq.squirrel_from_msa(msa, outgroup="Taxon1")
rooted.save("network_rooted.nwk")

Visualize (optional)

Plotting relies on PhyloZoo and requires the viz extra dependencies (pip install physquirrel[viz] or pip install physquirrel[graphviz]); see the Installation Guide.

from phylozoo.viz import plot

plot(network)

Next steps

• Manual — full workflow, all input types, and I/O options

• Installation — optional dependencies and building from source

• API Reference — complete API reference