Codon-Adaptation-Index-of-Species

This repository contains scripts, data, and methods of analysis used in the manuscript “The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder” (eLife2024;12:RP87335 DOI: https://doi.org/10.7554/eLife.87335.3).

Contents

CAIS_ENC_calculation:
Scripts used to calculate ENC, CAIS, and CAIS using local GC content

R_analysis_scripts_for_ISD_and_body_size:
R scripts used to analyize and plot data

R_pipeline_data:
datafiles used in R analysis and figure generation

Vertebrate_species_effects_ISD_paper:
data and scripts used to calculate ISD results

popgen_theory_code:
Population genetics theory models and scripts for Figure 1