MitoDate is a Nextflow pipeline for molecular clock dating of ancient mitochondrial genomes with BEAST, following the methodology published in Chacón-Duque et al., MBE (2025).
It can be used in three modes. tip_dating runs the main workflow from aligned FASTA, metadata, and priors. rerun_samples reruns selected samples from an earlier tip_dating run without starting over. joint_tree builds the final dated tree after you have reviewed the tip-dating results.
Example input files (10 representative samples from Chacón-Duque et al., MBE 2025) are provided in assets/test_data
Wenxi Li (wenxi.li@sund.ku.dk) Bilal Sharif (bilal.bioinfo@gmail.com)
If you use MitoDate in your research, please cite:
Li, W., Sharif, B., Heintzman, P. D., Dalén, L. and Chacón-Duque, J. C. 2026. MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes. – bioRxiv. : 2026.07.28.741234.