goe

A geological timescale for bacterial evolution and oxygen adaptation -- an McmcDate tutorial

Read the tutorial here or download the pdf version

File list

• tutorial_goe.md -- markdown version tutorial
• createpdf.sh -- a bash script to create a pdf version from the markdown file tutorial_goe.md
• tutorial_goe.pdf -- pdf version tutorial
• data/1007_mito_plastid.tree -- rooted species tree of Bacteria, inferred using 65 marker genes from 1007 genomes
• data/1007_mito_plastid.tree.unrooted -- unrooted species tree of Bacteria
• data/65genes_bac_and_organelles.phylip -- 65-gene concatenate including genes from the mitochondrial and plastid genomes
• data/braces.json -- bracin mitochondria and chloroplasts
• data/Fossils.csv -- fossil and geochemical calibrations
• data/XGBoost.csv -- fossil calibrations and aerobicity information based on the XGBoost classifier

The source of the data files is the publication Davín et al. A geological timescale for bacterial evolution and oxygen adaptation (2024)