Yanked
This release has been yanked by its maintainers, and will be ignored by installers, except when explicitly specified.
Consider using release 26.8.1 instead.
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()
1 maintainer
Metadata
1 maintainer
Release files for msasim 2024.5.221247
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| File | Size | Uploaded | |
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| msasim-2024.5.221247.tar.gz | 17.5 kB | Details |
Release files / msasim-2024.5.221247.tar.gz
| Download URL | msasim-2024.5.221247.tar.gz |
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