molecular-clock

Inferring global and local strict molecular clocks using root-to-tip regression

Explore Temporal and Other Phylogenetic Signals

Nextflow pipeline for estimation of evolutionary rate using Bayesian statistics.

Test for a molecular clock based on the phylogenetic tree inferred from single-cell DNA sequenzing data

Python framework for reproducible divergence time estimation with BEAST2: calibration prior specification, validation, and diagnostics

The PKS Test software was designed to directly verify whether a phylogeny is clock-like following a Poisson law.

Miscellaneous micro-projects from my Master’s degree focused on phylogenetics and evolution: Bayesian and maximum likelihood phylogenies, concatenated vs coalescent analyses, ancestral state reconstruction, divergence dating, gene flow, and substitution models.

Data and scripts to reproduce the molecular clock dating analyses presented in "Ancient bacterial genomes reveal a formerly unknown diversity of Treponema pallidum strains in early modern Europe (Majander et al.)

A Python toolkit for simulating sequence evolution and exploring molecular clock algorithms

Methods for the analyses described in Álvarez-Carretero et al. 2019 (https://doi.org/10.1093/sysbio/syz015)