README Each file in this folder contains a single dataset that was analysed to produce table 2 in the paper Refer to the manuscript to get the references for each dataset (the datasets themselves are publically available) Within each file there is: 1. An alignment file, from the original authors of the study 2. A PartitionFinder config file To rerun the analyses used to produce table 1: 1. Download and install PartitionFinder (to guard against changes in the config file format, it would be most reliable to use the version that was used for this study, which can be downloaded from here: https://github.com/brettc/partitionfinder/zipball/v0.9 2. Run PartitionFinder on each dataset with "search=all". This will tell you the best scheme overall 3. Run PartitionFinder on each dataset with "search=greedy". This will tell you the best dataset found by the greedy algorithm. 4. Run PartitionFinder on each dataset with "search=user". This will calculate scores for the different a-priori partitioning schemes (no partitioning, by gene, by codon, by gene and codon) listed at the end of each file.