Chronograms: Phylogenetic Tree of Life for Molecular Clock Analysis

A phylogenetic tree of life anchored in time with a molecular clock, created for evolutionary analysis. The dataset includes 865 genomes representing bacterial and archaeal diversity, constructed using maximum likelihood methodology on an alignment of sixteen ribosomal genes. It was created by Zhanghan Ni and last updated on May 14, 2026.

Use Cases

• Calibrating molecular clocks for gene family dating based on the provided phylogenetic tree and calibration points.
• Reconstructing deep evolutionary relationships among Bacteria and Archaea based on the 865-genome tree.
• Anchoring the evolutionary history of specific COGs (Clusters of Orthologous Groups) in geological time.

Strengths

• Includes 865 genomes chosen to represent the full diversity of Bacteria and Archaea.
• Tree construction uses sixteen ribosomal genes, a standard marker for deep evolutionary history.
• Molecular clock implemented with eight calibration points and a defined root prior.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect taxonomic bias inherent to the source genomes selected.

Provenance

Source

Zhanghan Ni via figshare

Collection Method

Phylogenetic tree created using GToTree and IQ-Tree 2.2.0.3; molecular clock implemented in PhyloBayes 4.1.

Freshness

Last updated 2026-05-14 00:10:09; freshness should be verified.