tsinfer

Infer a tree sequence from genetic variation data.

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

Science Score: 67.0%

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
Found 4 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
4 of 12 committers (33.3%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Infer a tree sequence from genetic variation data.

Basic Info

Host: GitHub
Owner: tskit-dev
License: gpl-3.0
Language: C
Default Branch: main
Homepage:
Size: 3.84 MB

Statistics

Stars: 60
Watchers: 11
Forks: 16
Open Issues: 108
Releases: 17

Created about 9 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

tsinfer

Infer a tree sequence from genetic variation data

The documentation contains details of how to use this software, including installation instructions.

The initial algorithm, its rationale, and results from testing on simulated and real data are described in the following Nature Genetics paper:

Jerome Kelleher, Yan Wong, Anthony W Wohns, Chaimaa Fadil, Patrick K Albers and Gil McVean (2019) Inferring whole-genome histories in large population datasets. Nature Genetics 51: 1330-1338

Tsinfer versions 0.2.0 onwards allow missing data and provide a fully parameterised Li & Stephens matching algorithm (i.e. which allows mismatch). These improvements are described in the following Science paper:

Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) A unified genealogy of modern and ancient genomes. Science 375: eabi8264

Please cite either or both of these if you use tsinfer in your work. Code to reproduce the results in the first paper is present in a separate GitHub repository.

Note that tsinfer does not attempt to infer node times (i.e. branch lengths of the inferred trees). If you require a tree sequence where the dates of common ancestors are expressed in calendar or generation times, you should post-process the tsinfer output using software such as tsdate.

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 tsinfer

If you use `tsinfer` in your work, please cite the
[2019 Nature Genetics paper](<https://doi.org/10.1038/s41588-019-0483-y>):

> Jerome Kelleher, Yan Wong, Anthony W. Wohns, 
> Chaimaa Fadil, Patrick K. Albers & Gil McVean (2019) 
> *Inferring whole-genome histories in large population datasets*,
> Nature Genetics, Volume 51, 1330–1338. https://doi.org/10.1038/s41588-019-0483-y

Bibtex record:

```bibtex

@article{Kelleher2019,
  doi = {10.1038/s41588-019-0483-y},
  url = {https://doi.org/10.1038/s41588-019-0483-y},
  year = {2019},
  month = sep,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {51},
  number = {9},
  pages = {1330--1338},
  author = {Jerome Kelleher and Yan Wong and Anthony W. Wohns and Chaimaa Fadil and Patrick K. Albers and Gil McVean},
  title = {Inferring whole-genome histories in large population datasets},
  journal = {Nature Genetics}
}
```

GitHub Events

Total

Create event: 5
Release event: 2
Issues event: 55
Watch event: 4
Delete event: 1
Issue comment event: 187
Push event: 36
Pull request review comment event: 56
Pull request review event: 79
Pull request event: 59
Fork event: 3

Last Year

Create event: 5
Release event: 2
Issues event: 55
Watch event: 4
Delete event: 1
Issue comment event: 187
Push event: 36
Pull request review comment event: 56
Pull request review event: 79
Pull request event: 59
Fork event: 3

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 1,135
Total Committers: 12
Avg Commits per committer: 94.583
Development Distribution Score (DDS): 0.381

Past Year

Commits: 117
Committers: 7
Avg Commits per committer: 16.714
Development Distribution Score (DDS): 0.573

Top Committers

Name	Email	Commits
Jerome Kelleher	jk@w****k	702
Yan Wong	y**n@y**e	151
Yan Wong	y**g@b**k	138
Ben Jeffery	b**y@b**k	43
dependabot[bot]	4**]@u**m	34
dependabot-preview[bot]	2**]@u**m	27
Ben Jeffery	b**y@g**m	16
Ben Jeffery	b**y@w**k	11
awohns	a**s@g**m	9
Shing Zhan	s**n@g**m	2
Inés Rebollo	4**o@u**m	1
dianali	d**z@g**m	1

Committer Domains (Top 20 + Academic)

bdi.ox.ac.uk: 2 well.ox.ac.uk: 2 yanwong.me: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 164
Total pull requests: 218
Average time to close issues: 11 months
Average time to close pull requests: about 1 month
Total issue authors: 16
Total pull request authors: 7
Average comments per issue: 2.99
Average comments per pull request: 3.72
Merged pull requests: 170
Bot issues: 0
Bot pull requests: 2

Past Year

Issues: 31
Pull requests: 77
Average time to close issues: 7 days
Average time to close pull requests: 5 days
Issue authors: 8
Pull request authors: 5
Average comments per issue: 2.0
Average comments per pull request: 1.94
Merged pull requests: 60
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

hyanwong (78)
benjeffery (41)
jeromekelleher (29)
awohns (3)
frezaei98 (2)
percyfal (1)
evolgenomics (1)
duncanMR (1)
nspope (1)
szhan (1)
tforest (1)
stsmall (1)
moshejasper (1)
Tatianabellagio (1)
bgyuris (1)

Pull Request Authors

benjeffery (118)
hyanwong (80)
jeromekelleher (14)
mergify[bot] (2)
duncanMR (2)
hossam26644 (1)
eaton-lab (1)

Top Labels

Issue Labels

enhancement (6) bug (5) documentation (1)

Pull Request Labels

AUTOMERGE-REQUESTED (34)

Packages

Total packages: 2
Total downloads:
- pypi 1,272 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 9
(may contain duplicates)
Total versions: 19
Total maintainers: 2

pypi.org: tsinfer

Infer tree sequences from genetic variation data.

Homepage: https://tskit.dev/tsinfer
Documentation: https://tskit.dev/tsinfer/docs/stable
License: GNU GPLv3+
Latest release: 0.4.1
published 12 months ago

Versions: 16
Dependent Packages: 1
Dependent Repositories: 8
Downloads: 1,272 Last month
Docker Downloads: 0

Rankings

Docker downloads count: 3.5%

Dependent packages count: 4.7%

Dependent repos count: 5.2%

Average: 6.0%

Downloads: 10.5%

Maintainers (2)

benjeffery jerome.kelleher

Last synced: 6 months ago

conda-forge.org: tsinfer

tsinfer infers succinct tree sequences from observed genetic variation data

Homepage: https://github.com/tskit-dev/tsinfer
License: GPL-3.0-or-later
Latest release: 0.3.0
published over 3 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Dependent repos count: 24.3%

Average: 40.4%

Stargazers count: 41.9%

Forks count: 43.8%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

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zarr ==2.11.3

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setup.py pypi

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sphinx-comments ==0.0.3
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tsinfer

Science Score: 67.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

tsinfer

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: tsinfer

Rankings

Maintainers (2)

conda-forge.org: tsinfer

Rankings

Dependencies