msprime

Simulate genealogical trees and genomic sequence data using population genetic models

https://github.com/tskit-dev/msprime

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
16 of 54 committers (29.6%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary

Keywords

coalescent genetics genomics msprime python simulation trees tskit

Keywords from Contributors

annotation closember parallel cryptocurrencies charts bioinformatics embedded distributed meshes interactive

Last synced: 4 months ago · JSON representation ·

Repository

Simulate genealogical trees and genomic sequence data using population genetic models

Basic Info

Host: GitHub
Owner: tskit-dev
License: gpl-3.0
Language: Python
Default Branch: main
Homepage:
Size: 15.3 MB

Statistics

Stars: 197
Watchers: 19
Forks: 89
Open Issues: 89
Releases: 62

Topics

coalescent genetics genomics msprime python simulation trees tskit

Created over 11 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog License Citation

msprime

msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consistent with a given demographic model) under a range of different models and evolutionary processes. Msprime can also simulate mutations on a given ancestral history (which can be produced by msprime or other programs supporting tskit) under a variety of genome sequence evolution models.

Please see the documentation for more details, including installation instructions.

Owner

Name: Tskit developers
Login: tskit-dev
Kind: organization
Email: admin@tskit.dev

Website: https://tskit.dev
Repositories: 26
Profile: https://github.com/tskit-dev

Software for the creation and analysis of tree-sequences.

Citation (CITATION.md)

(sec_citation)=

# Citing msprime

If you use `msprime` in your work, please cite the
[2022 Genetics paper](<https://doi.org/10.1093/genetics/iyab229>)
marking the 1.0 release:

> Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower,
> Aaron P Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E Castedo Ellerman,
> Jared G Galloway, Ariella L Gladstein, Gregor Gorjanc, Bing Guo,
> Ben Jeffery, Warren W Kretzschumar, Konrad Lohse, Michael Matschiner,
> Dominic Nelson, Nathaniel S Pope, Consuelo D Quinto-Cortés,
> Murillo F Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton,
> Hugo van Kemenade, Anthony W Wohns, Yan Wong, Simon Gravel, Andrew D Kern,
> Jere Koskela, Peter L Ralph and Jerome Kelleher (2022),
> *Efficient ancestry and mutation simulation with msprime 1.0*,
> Genetics, Volume 220, Issue 3. http://doi.org/10.1093/genetics/iyab229

You may also wish to cite the original
[2016 PLOS Computational Biology paper](<http://dx.doi.org/10.1371/journal.pcbi.1004842>):

> Jerome Kelleher, Alison M Etheridge and Gilean McVean (2016),
> *Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes*,
> PLOS Comput Biol 12(5): e1004842. doi: 10.1371/journal.pcbi.1004842

If you use the Discrete Time Wright Fisher model, please cite the
[2020 PLOS Genetics paper](https://doi.org/10.1371/journal.pgen.1008619):

> Dominic Nelson, Jerome Kelleher, Aaron P. Ragsdale, Claudia Moreau,
> Gil McVean and Simon Gravel (2020),
> *Accounting for long-range correlations in genome-wide simulations of large cohorts*,
> PLOS Genetics 16(5): e1008619. https://doi.org/10.1371/journal.pgen.1008619

Bibtex records:

```bibtex

@article{baumdicker2022efficient,
  title={Efficient ancestry and mutation simulation with msprime 1.0},
  author = {Baumdicker, Franz and Bisschop, Gertjan and Goldstein, Daniel
    and Gower, Graham and Ragsdale, Aaron P and Tsambos, Georgia and Zhu, Sha
    and Eldon, Bjarki and Ellerman, E Castedo and Galloway, Jared G
    and Gladstein, Ariella L and Gorjanc, Gregor and Guo, Bing
    and Jeffery, Ben and Kretzschumar, Warren W and Lohse, Konrad
    and Matschiner, Michael and Nelson, Dominic and Pope, Nathaniel S
    and Quinto-Cortés, Consuelo D and Rodrigues, Murillo F
    and Saunack, Kumar and Sellinger, Thibaut and Thornton, Kevin
    and van Kemenade, Hugo and Wohns, Anthony W and Wong, Yan
    and Gravel, Simon and Kern, Andrew D and Koskela, Jere
    and Ralph, Peter L and Kelleher, Jerome},
  journal={Genetics},
  volume={220},
  number={3},
  pages={iyab229},
  year={2022},
  publisher={Oxford University Press}
}

@article{kelleher2016efficient,
  title={Efficient coalescent simulation and genealogical analysis for large sample sizes},
  author={Kelleher, Jerome and Etheridge, Alison M and McVean, Gilean},
  journal={PLoS computational biology},
  volume={12},
  number={5},
  pages={e1004842},
  year={2016},
  publisher={Public Library of Science}
}

@article{nelson2020accounting,
  title={Accounting for long-range correlations in genome-wide simulations of large cohorts},
  author={Nelson, Dominic and Kelleher, Jerome and Ragsdale, Aaron P and
    Moreau, Claudia and McVean, Gil and Gravel, Simon},
  journal={PLoS genetics},
  volume={16},
  number={5},
  pages={e1008619},
  year={2020},
  publisher={Public Library of Science}
}
```

GitHub Events

Total

Create event: 17
Release event: 2
Issues event: 27
Watch event: 19
Delete event: 16
Issue comment event: 146
Push event: 44
Pull request review comment event: 11
Pull request review event: 18
Pull request event: 79
Fork event: 2

Last Year

Create event: 17
Release event: 2
Issues event: 27
Watch event: 19
Delete event: 16
Issue comment event: 146
Push event: 44
Pull request review comment event: 11
Pull request review event: 18
Pull request event: 79
Fork event: 2

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 3,060
Total Committers: 54
Avg Commits per committer: 56.667
Development Distribution Score (DDS): 0.296

Past Year

Commits: 52
Committers: 10
Avg Commits per committer: 5.2
Development Distribution Score (DDS): 0.654

Top Committers

Name	Email	Commits
Jerome Kelleher	jk@w****k	2,153
peter	p**p@g**m	237
Ben Jeffery	b**y@b**k	77
dependabot[bot]	4****]	63
Dominic Nelson	n**c@g**m	51
Graham Gower	g**r@g**m	48
Yan Wong	y**g@b**k	42
dependabot-preview[bot]	2****]	35
JereKoskela	j**a@w**k	30
Jaime Ashander	j**r@u**u	28
Jere Koskela	J**a@w**k	24
Gertjan Bisschop	g**p@g**m	22
andrewkern	a**n@u**u	22
Michael Matschiner	m**r@m**m	22
Franz Baumdicker	f**r@g**e	21
Joe Zhu	s**u@g**m	19
Georgia Tsambos	g**s@s**u	14
molpopgen	k**t@u**u	12
Daniel Goldstein	d**5@g**m	12
Castedo Ellerman	c**o@c**m	11
Aaron Ragsdale	a**e@m**a	9
Ben Jeffery	b**y@w**k	8
gbinux	g**x@g**m	8
Yan Wong	y**n@y**e	7
Nik Baya	n**a@g**m	7
Warren Kretzschmar	w**r@k**e	7
Consuelo Quinto	c**o@g**m	6
TPPSellinger	5****r	5
Hugo	h****k	5
Ariella Gladstein	a**n@g**m	5
and 24 more...

Committer Domains (Top 20 + Academic)

well.ox.ac.uk: 2 bdi.ox.ac.uk: 2 warwick.ac.uk: 2 ucdavis.edu: 1 uoregon.edu: 1 mac.com: 1 gmx.de: 1 student.unimelb.edu.au: 1 uci.edu: 1 castedo.com: 1 mail.mcgill.ca: 1 yanwong.me: 1 ki.se: 1 wisc.edu: 1 email.arizona.edu: 1 utexas.edu: 1 pixie.org.uk: 1 colorado.edu: 1 mcgill.ca: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 127
Total pull requests: 209
Average time to close issues: 7 months
Average time to close pull requests: 13 days
Total issue authors: 42
Total pull request authors: 20
Average comments per issue: 3.54
Average comments per pull request: 2.99
Merged pull requests: 158
Bot issues: 1
Bot pull requests: 6

Past Year

Issues: 18
Pull requests: 66
Average time to close issues: 6 days
Average time to close pull requests: 2 days
Issue authors: 9
Pull request authors: 10
Average comments per issue: 0.67
Average comments per pull request: 2.42
Merged pull requests: 39
Bot issues: 1
Bot pull requests: 6

View more stats

Top Authors

Issue Authors

jeromekelleher (50)
GertjanBisschop (9)
hyanwong (8)
daikitag (5)
benjeffery (4)
nspope (3)
andrewkern (3)
isaacovercast (2)
molpopgen (2)
trevorcousins (2)
connor-french (2)
YuanboSong (2)
tomwhite (2)
yzliu01 (2)
petrelharp (2)

Pull Request Authors

benjeffery (64)
GertjanBisschop (34)
jeromekelleher (33)
hyanwong (18)
petrelharp (13)
JereKoskela (6)
hossam26644 (6)
mergify[bot] (6)
andrewkern (6)
daikitag (6)
abureau (4)
not-a-feature (2)
hannesbecher (2)
agushin101 (2)
apragsdale (2)

Top Labels

Issue Labels

enhancement (11) bug (9) documentation (7) Infrastructure and tools (7) Performance (5) help wanted (1) question (1)

Pull Request Labels

AUTOMERGE-REQUESTED (21) documentation (2)

Packages

Total packages: 2
Total downloads:
- pypi 15,674 last-month

Total dependent packages: 19
(may contain duplicates)
Total dependent repositories: 109
(may contain duplicates)
Total versions: 77
Total maintainers: 2

pypi.org: msprime

Simulate genealogical trees and genomic sequence data using population genetic models

Homepage: https://tskit.dev/msprime
Documentation: https://tskit.dev/msprime/docs/stable
License: GNU GPLv3+
Latest release: 1.3.4
published 8 months ago

Versions: 61
Dependent Packages: 16
Dependent Repositories: 83
Downloads: 15,674 Last month
Docker Downloads: 0

Rankings

Dependent packages count: 0.8%

Dependent repos count: 1.6%

Average: 2.1%

Downloads: 2.4%

Docker downloads count: 3.6%

Maintainers (2)

benjeffery jerome.kelleher

Last synced: 4 months ago

conda-forge.org: msprime

Simulate genealogical trees and genomic sequence data using population genetic models

Homepage: http://pypi.python.org/pypi/msprime
License: GPL-3.0-or-later
Latest release: 1.2.0
published over 3 years ago

Versions: 16
Dependent Packages: 3
Dependent Repositories: 26

Rankings

Dependent repos count: 7.2%

Dependent packages count: 15.6%

Average: 18.2%

Forks count: 20.6%

Stargazers count: 29.4%

Last synced: 4 months ago

Dependencies

.github/workflows/docs.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-python v2 composite
styfle/cancel-workflow-action 0.6.0 composite

.github/workflows/tests.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-python v2 composite
conda-incubator/setup-miniconda v2 composite
pre-commit/action v2.0.0 composite
styfle/cancel-workflow-action 0.6.0 composite

.github/workflows/wheels.yml actions

actions/checkout v2 composite
actions/download-artifact v2 composite
actions/setup-python v2 composite
actions/upload-artifact v2 composite
pypa/gh-action-pypi-publish master composite

requirements/CI-complete/requirements.txt pypi

bintrees ==2.2.0
codecov ==2.1.12
daiquiri ==3.0.1
demes ==0.2.1
jsonschema <4.0
kastore ==0.3.2
mypy ==0.910
newick ==1.3.2
numpy ==1.21.4
pytest ==6.2.5
pytest-cov ==3.0.0
pytest-xdist ==2.5.0
python_jsonschema_objects ==0.4.1
scipy ==1.7.3
stdpopsim ==0.1.2
tskit ==0.5.3

requirements/CI-docs/requirements.txt pypi

daiquiri ==3.0.1
demes ==0.2.1
demesdraw ==0.2.0
jupyter-book ==0.13.0
matplotlib ==3.5.0
networkx ==2.6.3
newick ==1.3.1
sphinx-argparse ==0.3.1
sphinx-issues ==1.2.0
tskit ==0.5.3
tskit-book-theme ==0.3.2

requirements/CI-tests-conda/requirements.txt pypi

demes ==0.2.1 test
gsl * test
jsonschema <4.0 test
stdpopsim ==0.1.2 test
tskit ==0.5.3 test

requirements/CI-tests-pip/requirements.txt pypi

bintrees ==2.2.0 test
daiquiri ==3.0.1 test
jsonschema <5.0 test
newick ==1.3.1 test
numpy ==1.21.4 test
pytest ==6.2.5 test
pytest-xdist ==2.4.0 test
python_jsonschema_objects ==0.4.1 test
scipy ==1.7.3 test
tskit ==0.5.3 test

requirements/development.txt pypi

asv * development
bintrees * development
codecov * development
coverage * development
daiquiri * development
demes >=0.2.0 development
demesdraw * development
flake8 * development
jsonschema <4.0 development
jupyter-book * development
matplotlib >=3.4.0 development
meson >=0.61.0 development
mock * development
mypy * development
networkx * development
newick >=1.3.0 development
ninja * development
numpy * development
pre-commit * development
pytest * development
pytest-cov * development
pytest-xdist * development
python_jsonschema_objects * development
scipy * development
setuptools_scm * development
sphinx >=4.4 development
sphinx-argparse * development
sphinx-issues * development
stdpopsim >=0.1.2 development
tskit >=0.5.2 development
tskit-book-theme * development

requirements/verification.txt pypi

argparse *
daiquiri *
dendropy *
matplotlib *
numpy *
pandas *
pyslim *
pyvolve *
scikit-allel *
scipy ==1.2
seaborn *
statsmodels *
tqdm *

msprime

Science Score: 54.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

msprime

Owner

Citation (CITATION.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: msprime

Rankings

Maintainers (2)

conda-forge.org: msprime

Rankings

Dependencies