taxonium-component

A tool for exploring large trees in the browser

https://github.com/theosanderson/taxonium

Science Score: 77.0%

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 3 DOI reference(s) in README
✓
Academic publication links
Links to: biorxiv.org, pubmed.ncbi, ncbi.nlm.nih.gov
✓
Committers with academic emails
4 of 13 committers (30.8%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary

Keywords

deckgl phylogenetics phylogeny react tree virus

Keywords from Contributors

batteries interpretability energy-system jax energy-system-model data-profiling histogram redoc mesh animations

Last synced: 6 months ago · JSON representation ·

Repository

A tool for exploring large trees in the browser

Basic Info

Host: GitHub
Owner: theosanderson
License: gpl-3.0
Language: TypeScript
Default Branch: master
Homepage: http://taxonium.org
Size: 260 MB

Statistics

Stars: 114
Watchers: 6
Forks: 22
Open Issues: 115
Releases: 127

Topics

deckgl phylogenetics phylogeny react tree virus

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Citation

Taxonium

Taxonium is a tool for exploring trees, including those with millions of nodes.

How do I..

visualise my own Newick phylogeny?

Upload a Newick file to Taxonium.org, and optionally a metadata file in CSV or TSV format. If using a metadata file the leftmost column must contain names of the nodes as in the tree.

explore the global SARS-CoV-2 phylogeny?

Visit Cov2Tree.org which uses Taxonium to allow you to explore a tree built by researchers at UCSC using public data contributed by researchers across the world to the INSDC databases.

build my own mutation-annotated tree to explore in Taxonium, or add my own metadata to an existing phylogeny?

Use UShER to build a mutation-annotated tree. Then use taxoniumtools to convert it to a Taxonium format you can upload to the interface at Taxonium.org

You can also use taxoniumtools to add your own metadata to the existing public phylogeny.

Find out more in 📚 the documentation.

load really huge trees?

For trees larger than about 6M tips, loading local trees in the browser at Taxonium.org can be unreliable on some systems due to browser memory limitations. To avoid these issues, use the Taxonium desktop app.

use Taxonium in my own web application?

Use the Taxonium component.

See Taxonium in action

Cov2Tree - (the repo that runs this is here)
Exploring the NCBI Taxonomy
Serratus (click Tree Viewer on any tree)

Citing Taxonium

Sanderson, T (2022). Taxonium, a web-based tool for exploring large phylogenetic trees. eLife, 11:e82392 https://doi.org/10.7554/eLife.82392

N.B. If you are citing the tree displayed at Cov2Tree.org, please cite the UCSC tree (.. and ideally Taxonium too if you relied on it for exploration)

There is a separate paper for the Treenome Browser feature (Kramer et al., Bioinformatics, 2022).

Structure

Taxonium is structured as a 'monorepo' containing a number of components:

taxoniumtools - a Python package that lets you easily generate Taxonium files from Usher protobuf files
taxonium_component - a React component that implements the Taxonium tree explorer
taxonium_website - The Taxonium website found at Taxonium.org, a wrapper around taxonium_component
taxonium_backend - a server-based backend that allows Taxonium trees to be explored without the user downloading the full tree (N.B. Taxonium can also be used without this backend, with static files acccessed in taxonium_website)
taxoniumdatahandling - this is a node package upon which both the web client and the backend depend (it handles core logic common to both)

Contributing

We welcome contributions. We require that that all contributors follow the Contributor Covenant Code of Conduct.

Contributors

Taxonium development was initiated and is led by Theo Sanderson at the Francis Crick Institute.

_{Theo Sanderson}
💻 📖 🎨 🤔 🚇 🚧

We are very grateful to our contributors:

_{Alex Kramer}
💻 🎨 🤔

_{Angie Hinrichs}
🤔 🔣 💻

_{Richard Goater}
🎨 💻

_{Chaoran Chen}
🤔

_{Cornelius Roemer}
🤔

_{Sung Kwon}
🚇

_{Koorous Vargha}
💻

Alex Kramer at UCSC built the Treenome Browser component within Taxonium, described here.

Owner

Name: Theo Sanderson
Login: theosanderson
Kind: user
Location: London, UK
Company: London School of Hygiene & Tropical Medicine

Website: http://theo.io
Twitter: theosanderson
Repositories: 156
Profile: https://github.com/theosanderson

Full stack pathogen geneticist

Citation (CITATION.bib)

@article {10.7554/eLife.82392,
article_type = {journal},
title = {Taxonium, a web-based tool for exploring large phylogenetic trees},
author = {Sanderson, Theo},
volume = 11,
year = 2022,
month = {nov},
pub_date = {2022-11-15},
pages = {e82392},
citation = {eLife 2022;11:e82392},
doi = {10.7554/eLife.82392},
url = {https://doi.org/10.7554/eLife.82392},
abstract = {The COVID-19 pandemic has resulted in a step change in the scale of sequencing data, with more genomes of SARS-CoV-2 having been sequenced than any other organism on earth. These sequences reveal key insights when represented as a phylogenetic tree, which captures the evolutionary history of the virus, and allows the identification of transmission events and the emergence of new variants. However, existing web-based tools for exploring phylogenies do not scale to the size of datasets now available for SARS-CoV-2. We have developed Taxonium, a new tool that uses WebGL to allow the exploration of trees with tens of millions of nodes in the browser for the first time. Taxonium links each node to associated metadata and supports mutation-annotated trees, which are able to capture all known genetic variation in a dataset. It can either be run entirely locally in the browser, from a serverbased backend, or as a desktop application. We describe insights that analysing a tree of five million sequences can provide into SARS-CoV-2 evolution, and provide a tool at cov2tree.org for exploring a public tree of more than five million SARS-CoV-2 sequences. Taxonium can be applied to any tree, and is available at taxonium.org, with source code at github.com/theosanderson/taxonium.},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}

GitHub Events

Total

Create event: 98
Release event: 16
Issues event: 24
Watch event: 9
Delete event: 45
Issue comment event: 143
Push event: 378
Pull request review comment event: 1
Pull request review event: 3
Pull request event: 137
Fork event: 4

Last Year

Create event: 98
Release event: 16
Issues event: 24
Watch event: 9
Delete event: 45
Issue comment event: 143
Push event: 378
Pull request review comment event: 1
Pull request review event: 3
Pull request event: 137
Fork event: 4

Committers

Last synced: 9 months ago

All Time

Total Commits: 2,156
Total Committers: 13
Avg Commits per committer: 165.846
Development Distribution Score (DDS): 0.15

Past Year

Commits: 61
Committers: 3
Avg Commits per committer: 20.333
Development Distribution Score (DDS): 0.066

Top Committers

Name	Email	Commits
Theo Sanderson	t**o@s**k	1,832
github-actions	4****]	150
pre-commit-ci[bot]	6****]	54
Alex Kramer	a**r@u**u	53
github-actions	g**s@g**m	29
allcontributors[bot]	4****]	15
Alex Kramer	a**e@u**u	13
Richard Goater	r**9@s**k	3
Angie Hinrichs	a**e@s**u	3
Sung Kwon	s**n@t**i	1
Sehi L'Yi	s**i@g**m	1
Koorous Vargha	3****a	1
Cornelius Roemer	c**r@g**m	1

Committer Domains (Top 20 + Academic)

ucsc.edu: 2 tractable.ai: 1 soe.ucsc.edu: 1 sanger.ac.uk: 1 github.com: 1 sndrsn.co.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 117
Total pull requests: 309
Average time to close issues: 25 days
Average time to close pull requests: 8 days
Total issue authors: 23
Total pull request authors: 10
Average comments per issue: 2.68
Average comments per pull request: 1.24
Merged pull requests: 191
Bot issues: 0
Bot pull requests: 19

Past Year

Issues: 21
Pull requests: 176
Average time to close issues: 7 days
Average time to close pull requests: 3 days
Issue authors: 9
Pull request authors: 4
Average comments per issue: 1.71
Average comments per pull request: 1.13
Merged pull requests: 89
Bot issues: 0
Bot pull requests: 16

View more stats

Top Authors

Issue Authors

theosanderson (40)
corneliusroemer (36)
AngieHinrichs (14)
GuilhemSempere (4)
chaoran-chen (4)
UTNK (3)
Sanyukta2001 (2)
aofarrel (2)
liamxg (2)
kvargha (1)
alex1770 (1)
Biophylo2001 (1)
martinghunt (1)
NicolaDM (1)
singing-scientist (1)

Pull Request Authors

theosanderson (296)
dependabot[bot] (15)
AngieHinrichs (5)
amkram (4)
allcontributors[bot] (3)
simonbukin (2)
pre-commit-ci[bot] (1)
DLiarakos (1)
richardgoater (1)
sehilyi (1)
corneliusroemer (1)
kvargha (1)

Top Labels

Issue Labels

help wanted (1)

Pull Request Labels

codex (74) dependencies (15) github_actions (15)

Packages

Total packages: 2
Total downloads:
- pypi 1,913 last-month
- npm 2,268 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 148
Total maintainers: 1

npmjs.org: taxonium-component

React component for exploring large phylogenetic trees in the browser

Homepage: https://github.com/theosanderson/taxonium#readme
License: gpl-3.0
Latest release: 2.1.12
published 6 months ago

Versions: 41
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 2,268 Last month

Rankings

Stargazers count: 5.3%

Forks count: 6.0%

Dependent repos count: 10.4%

Downloads: 10.4%

Average: 16.8%

Dependent packages count: 52.1%

Maintainers (1)

theosanderson

Last synced: 6 months ago

pypi.org: taxoniumtools

Generate files for taxonium

Homepage: https://github.com/theosanderson/taxonium
Documentation: https://taxoniumtools.readthedocs.io/
License: MIT License
Latest release: 2.1.10
published 7 months ago

Versions: 107
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 1,913 Last month

Rankings

Stargazers count: 7.8%

Dependent packages count: 10.1%

Forks count: 10.2%

Downloads: 11.9%

Average: 21.4%

Dependent repos count: 67.4%

Maintainers (1)

theosanderson

Last synced: 6 months ago

Dependencies

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.devcontainer/Dockerfile docker

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taxonium_backend/package.json npm

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axios ^0.26.1
commander ^9.1.0
compression ^1.7.4
cors ^2.8.5
express ^4.17.3
express-queue ^0.0.13
node-fetch ^3.2.10
pako ^2.0.4
taxonium_data_handling file:../taxonium_data_handling
xml2js ^0.4.23

taxonium_backend/yarn.lock npm

@jsonlines/core 1.0.2
accepts 1.3.8
array-flatten 1.1.1
axios 0.26.1
body-parser 1.19.2
bytes 3.0.0
bytes 3.1.2
commander 9.1.0
compressible 2.0.18
compression 1.7.4
content-disposition 0.5.4
content-type 1.0.4
cookie 0.4.2
cookie-signature 1.0.6
core-js 3.22.2
cors 2.8.5
data-uri-to-buffer 4.0.0
debug 2.6.9
debug 4.3.4
debug 3.2.7
depd 1.1.2
destroy 1.0.4
ee-first 1.1.1
encodeurl 1.0.2
escape-html 1.0.3
etag 1.8.1
express 4.17.3
express-end 0.0.8
express-queue 0.0.13
fetch-blob 3.2.0
finalhandler 1.1.2
follow-redirects 1.14.9
formdata-polyfill 4.0.10
forwarded 0.2.0
fresh 0.5.2
http-errors 1.8.1
iconv-lite 0.4.24
inherits 2.0.4
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media-typer 0.3.0
merge-descriptors 1.0.1
methods 1.1.2
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mime-db 1.52.0
mime-types 2.1.35
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ms 2.0.0
ms 2.1.2
ms 2.1.3
negotiator 0.6.3
node-domexception 1.0.0
node-fetch 3.2.10
object-assign 4.1.1
on-finished 2.3.0
on-headers 1.0.2
pako 2.0.4
parseurl 1.3.3
path-to-regexp 0.1.7
proxy-addr 2.0.7
qs 6.9.7
range-parser 1.2.1
raw-body 2.4.3
readable-stream 3.6.0
readable-web-to-node-stream 3.0.2
safe-buffer 5.1.2
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safer-buffer 2.1.2
sax 1.2.4
send 0.17.2
serve-static 1.14.2
setprototypeof 1.2.0
statuses 1.5.0
string_decoder 1.3.0
taxonium_data_handling 1.0.1
toidentifier 1.0.1
type-is 1.6.18
unpipe 1.0.0
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utils-merge 1.0.1
vary 1.1.2
web-streams-polyfill 3.2.1
xml2js 0.4.23
xmlbuilder 11.0.1

taxonium_data_handling/package.json npm

readable-web-to-node-stream ^3.0.2

taxonium_data_handling/yarn.lock npm

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readable-web-to-node-stream 3.0.2
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taxonium_electron/package.json npm

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electron ^21.1.0 development
electron-squirrel-startup ^1.0.0
taxonium_backend file:../taxonium_backend

taxonium_electron/yarn.lock npm

553 dependencies

taxonium_web_client/package.json npm

eslint-config-standard ^16.0.3 development
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eslint-plugin-promise ^5.1.0 development
postcss 8 development
@craco/craco ^6.1.2
@fontsource/roboto ^4.5.5
@jbrowse/plugin-data-management ^2.1.4
@jbrowse/react-linear-genome-view ^2.1.4
@tailwindcss/forms ^0.5.2
@testing-library/jest-dom ^5.11.4
@testing-library/react ^11.1.0
@testing-library/user-event ^12.1.10
JSONStream ^1.3.5
autoprefixer ^9
axios ^0.27.2
binary-search ^1.3.6
classnames ^2.3.1
commander ^9.0.0
compression ^1.7.4
cors ^2.8.5
craco ^0.0.3
deck.gl ^8.6.6
jsonl ^1.1.2
lodash ^4.17.21
lzma-native ^8.0.6
node-polyfill-webpack-plugin ^1.1.4
pako ^2.0.4
process ^0.11.10
react ^17.0.2
react-circular-progressbar ^2.0.4
react-debounce-input ^3.2.3
react-dom ^17.0.2
react-hot-toast ^2.2.0
react-icons ^4.6.0
react-modal ^3.15.1
react-router-dom ^5.2.0
react-scripts 5.0.0
react-spinners ^0.11.0
react-tooltip ^4.2.21
readable-web-to-node-stream ^3.0.2
scale-color-perceptual ^1.1.2
tailwindcss >=3.1.0
taxonium_data_handling file:../taxonium_data_handling
web-vitals ^1.0.1
webpack ^5.72.0
yargs ^17.3.1

taxonium_web_client/yarn.lock npm

1853 dependencies

docs/requirements.txt pypi

alive-progress *
biopython *
furo *
google-api-python-client *
myst-parser *
orjson *
pandas *
protobuf <4
sphinx-argparse *
sphinx-book-theme *
sphinx-rtd-theme *
sphinxcontrib-gtagjs *
treeswift *