1. Whole-tree dN/dS and overall substitution rates analysis

This folder contains the input and output files used in and obtained from the program PAML (Yang 2007) for the whole-tree analysis of dN/dS ratios (program component codeml) and overall substitution rates (program component baseml). This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Note both analyses types (codeml and baseml) use the same tree and nucleotide files. Each gene folder contains 6 files: 2 control files (1 codeml, 1 baseml - “.ctl”), 1 nucleotide file (“.nuc”), 1 tree file (“.trees”), 2 output files (1 codeml, 1 baseml).