Generate simulated phylogenetic data using DendroPy

simulate.py

import dendropy
from dendropy.simulate import treesim
from dendropy.model.discrete import Hky85, simulate_discrete_char_dataset

# Generate a simulated tree
taxa = dendropy.TaxonNamespace(['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h'])
tree_model = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, taxon_namespace=taxa)

# Use the HKY85 model for character mutation
seq_model = Hky85()

# Simulate a data set with the given tree and model, with 50 character sequences
data = simulate_discrete_char_dataset(50, tree_model, seq_model)

# Print tree and sequences in FASTA format
tree_model.print_plot()
print(data.as_string('fasta'))