# Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression ## Files in this repo 1. simStudy.R - R script to produce the simulation study. 2. simStudyData.RData - The compressed data produced by simStudy.R. Load this file if you want to reproduce the analysis, but don't want to regenerate all the data yourself. This is a convenience file. 3. testTrees.R - R script to produce the trees used as test cases for the simulation study of the clock search feature 4. clockSearchWrapper.ts - TypeScript file that call the clockSearch function from the main Clockor2 repo for use in the simulation study. Further details in lines 1-9 to run. Configuration can be difficult. See further the an example config.ts file. ## About Welcome to the Clockor2 code base! The Clockor2 app is available at [clockor2.github.io](https://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](https://clockor2.github.io/docs) for more information. Clockor2 is open-source and licensed under the [GNU General Public License v3.0](https://github.com/clockor2/clockor2/blob/main/LICENSE). We welcome contributions, feature requests, and bug reports. See below for a guide on developing Clockor2. ## Citation > Featherstone, L. A., Rambaut, A., Duchene, S., & Wirth, W. (2023). Inferring global and local strict molecular clocks using root-to-tip regression. bioRxiv. ## Development Clockor2 is built with [Create React App](https://github.com/facebook/create-react-app), using the [Redux](https://redux.js.org/) and [Redux Toolkit](https://redux-toolkit.js.org/) TS template. To get started clone the repo and install the dependencies. bash git clone https://github.com/clockor2/clockor2.git && cd clockor2 npm install Start the development server for local development. bash npm run start Run test with [jest](https://jestjs.io/) bash npm run test Some of the tools used by the project include: * React - * Flowbite - * Redux - * Phylocanvas - * Plotly - * phylojs - The initial design plan: This is an optional, freeform section for describing any code in your submission and the software used to run it. Describe any scripts, code, or notebooks (e.g., R, Python, Mathematica, MatLab) as well as the software versions (including loaded packages) that you used to run those files. If your repository contains more than one file whose relationship to other scripts is not obvious, provide information about the workflow that you used to run those scripts and notebooks.

Molecular sequence data from rapidly evolving organisms are often sampled at different points in time. Sampling times can then be used for molecular clock calibration. The root-to-tip (RTT) regression is an essential tool to assess the degree to which the data behave in a clock-like fashion. Here, we introduce Clockor2, a client-side web application for conducting RTT regression. Clockor2 uniquely allows users to quickly fit local and global molecular clocks, thus handling the increasing complexity of genomic datasets that sample beyond the assumption homogeneous host populations. Clockor2 is efficient, handling trees of up to the order of 10^4 tips, with significant speed increases compared to other RTT regression applications. Although clockor2 is written as a web application, all data processing happens on the client-side, meaning that data never leaves the user's computer. Clockor2 is freely available at https://clockor2.github.io/