Welcome to the Lacerta viridis mitogenome repository!

This repository is a collection of several scripts and mini-tutorials guiding you through the methods and analyses which were performed in the paper by Jauss et al., 2021.

The raw data can be downloaded here, plots and figures were generated with the final trees and miscellaneous files accessible in the folder 00_Data.

Relevant scripts and tutorials can be found in the corresponding markdown files, which are linked and highlighted for each category.

This folder contains the trees and miscellaneous data used for the subsequent analyses and visualisations. Intermediate files are not provided here, but you can generate them yourself by following the next steps.

In this pipeline, you find the neccessary scripts to generate the phylogenetic trees from raw .fastq files.

In this folder you find all input and output files for the constrained topology analysis performed with iqtree. The constraints were performed with RAxML based on the topologies indicated in the two text files.

This is a collection of several scripts neccessary for the visualisation of the phylogeny, biogeography and sequence motif evolution:

• Plot the phylogenetic tree and project it on a geographic map
• Project the pairwise distance in a heatmap
• Visualise the mitochondrial control region
• Plot the sequence motif evolution