msasim 2024.5.221253

A fast MSA simulator

Sailfish

Sailfish is a performant multiple sequence alignment(MSA) simulator, written in C++ and Python, allowing for quick and easy generation of large simulated datasets.

Project goals

• Ease of use
• Speed
• Modularity

Installation

pip install msasim

Example

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()