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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 2024.5.221251
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| msasim-2024.5.221251-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.17+ x86-64 | Details |
| msasim-2024.5.221251-cp312-cp312-macosx_11_0_arm64.whl | CPython 3.12 | CPython 3.12 | macOS 11.0+ ARM64 | Details |
| msasim-2024.5.221251-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.17+ x86-64 | Details |
| msasim-2024.5.221251-cp311-cp311-macosx_11_0_arm64.whl | CPython 3.11 | CPython 3.11 | macOS 11.0+ ARM64 | Details |
| msasim-2024.5.221251-cp37-cp37m-win_amd64.whl | CPython 3.7 | CPython 3.7 pymalloc | Windows x86-64 | Details |
| msasim-2024.5.221251-cp37-cp37m-macosx_10_9_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | macOS 10.9+ x86-64 | Details |
Total release size: 2.2 MB
Release files / msasim-2024.5.221251-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | msasim-2024.5.221251-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 432.2 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Yes |
| Uploaded via |
twine/5.0.0 CPython/3.12.3
|
Release files / msasim-2024.5.221251-cp312-cp312-macosx_11_0_arm64.whl
| Download URL | msasim-2024.5.221251-cp312-cp312-macosx_11_0_arm64.whl |
|---|---|
| Size | 347.4 kB |
| Tags | CPython 3.12 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
twine/5.0.0 CPython/3.12.3
|
Release files / msasim-2024.5.221251-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | msasim-2024.5.221251-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 433.6 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
twine/5.0.0 CPython/3.12.3
|
Release files / msasim-2024.5.221251-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | msasim-2024.5.221251-cp311-cp311-macosx_11_0_arm64.whl |
|---|---|
| Size | 347.2 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
twine/5.0.0 CPython/3.12.3
|
Release files / msasim-2024.5.221251-cp37-cp37m-win_amd64.whl
| Download URL | msasim-2024.5.221251-cp37-cp37m-win_amd64.whl |
|---|---|
| Size | 235.1 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Windows x86-64 |
|
SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
twine/5.0.0 CPython/3.12.3
|
Release files / msasim-2024.5.221251-cp37-cp37m-macosx_10_9_x86_64.whl
| Download URL | msasim-2024.5.221251-cp37-cp37m-macosx_10_9_x86_64.whl |
|---|---|
| Size | 376.7 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc macOS 10.9+ x86-64 |
|
SHA-256 checksum How to use checksums |
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| Uploaded via |
twine/5.0.0 CPython/3.12.3
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