Welcome to the Clockor2 code base! The Clockor2 app is available at clockor2.github.io.

Clockor2 is a client-side web application for conducting root-to-tip (RTT) regression - the fastest and most widely used method to calibrate strict molecular clocks. See the documentation for more information.

Clockor2 is open-source and licensed under the GNU General Public License v3.0. We welcome contributions, feature requests, and bug reports. See below for a guide on developing Clockor2.

Citation

Leo A Featherstone, Andrew Rambaut, Sebastian Duchene, Wytamma Wirth, Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression, Systematic Biology, 2024;, syae003, https://doi.org/10.1093/sysbio/syae003

Development

Clockor2 is built with Create React App, using the Redux and Redux Toolkit TS template.

To get started clone the repo and install the dependencies.

git clone https://github.com/clockor2/clockor2.git && cd clockor2
npm install

Start the development server for local development.

npm run start

Run test with jest

npm run test

Some of the tools used by the project include:

• React - https://www.youtube.com/watch?v=s2skans2dP4&ab_channel=DennisIvy
• Flowbite - https://flowbite-react.com/
• Redux - https://react-redux.js.org/tutorials/quick-start
• Phylocanvas - https://gitlab.com/cgps/phylocanvas/phylocanvas.gl
• Plotly - https://github.com/plotly/react-plotly.js
• phylojs - https://github.com/clockor2/phylojs

The initial design plan:

Docs

For docs code see https://github.com/clockor2/docs.

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