MetaClock

MetaClock is an integrated framework for reconstructing time-resolved evolutionary history for microbial genomes using large-scale (meta)genomics data from ancient and contemporary samples.

Main features

• Automated reconstruction of whole-genome alignment from large-scale metagenomics data using multiple reference genomes
• Automated authentication for ancient DNA origin, damaged sites removal, SNV analysis etc.
• Rich utilities for manual curation to enhance the quality of phylogenetic and molecular dating analysis

Installation

Bioconda

You can install MetaClock in an isolated environment using conda as follows:

conda create -n mc -c bioconda metaclock

conda activate mc

Private conda channel

Temporarily, you can install MetaClock through a private conda channel. But this option will be replaced once bioconda channel is ready.

conda create -n metaclock -c khuang16 -c compbiocore -c kantorlab -c bioconda -c conda-forge metaclock

Due to the dependency bowtie2 is encountering tbb-related issue, after metaclock installation is completed please manually install tbb library as described below:

conda activate metaclock

conda install tbb=2020.2

Repository

You can clone the MetaClock repository from GitHub:

git clone https://github.com/SegataLab/metaclock.git

Dependencies:

Tutorials

• MetaClock User manual
• MetaClock Tutorials

Support

Please post your issues in our metaclock issues section

Citation

If you think our tool is helpful for your research please cite https://github.com/SegataLab/metaclock. Note: citation source will be updated soon when manuscript is published. Thank you for your patience!