DOI: 10.5061/dryad.gxd2547sn
title: Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression

description: 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/
description: # 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 &gt; 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.