Sailfish is a performant multiple sequence alignment(MSA) simulator, written in C++ and Python, allowing for quick and easy generation of large simulated datasets.
pip install msasim
from msasim import sailfish as sim
from msasim.sailfish import MODEL_CODES, ZipfDistribution
ROOT_SEQUENCE_LENGTH = 100
sim_protocol = sim.SimProtocol("(A:0.5,B:0.5);",
deletion_rate=0.01,
insertion_rate=0.01,
deletion_dist=ZipfDistribution(1.08, 50),
insertion_dist=ZipfDistribution(1.08, 50),
seed=50)
sim_protocol.set_sequence_size(ROOT_SEQUENCE_LENGTH)
simulation = sim.Simulator(sim_protocol, simulation_type=sim.SIMULATION_TYPE.PROTEIN)
simulation.set_replacement_model(model=MODEL_CODES.WAG,
gamma_parameters_alpha=1.0,
gamma_parameters_catergories=4)
msa = simulation()
msa.print_msa()
FAQs
A fast MSA simulator
We found that msasim demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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