Code and data for: Synonymous substitution rates of nuclear-encoded mitochondria-related genes negatively correlate with maximum lifespan in ray-finned fishes

Code and data for the article “Synonymous substitution rates of nuclear-encoded mitochondria-related genes negatively correlate with maximum lifespan in ray-finned fishes” by Takayoshi Otsuka and Hideaki Matsui. The record contains the scripts and the intermediate and final results of the analyses of 85 ray-finned fish species and the outgroup Latimeria chalumnae. The deposited data are sufficient to regenerate all figures and Supplementary Tables S3–S13 without querying NCBI or rerunning BLAST and codeml. Files README.md: contents, software requirements and the commands to run. code.zip: Python, R and shell scripts, one folder per analysis step. data.zip: species list and phylogenies; gene list; ortholog identification and validation, including the blastp results and the manual review decisions; amino acid and codon alignments of the nuclear-encoded and the 13 mtDNA-encoded genes; codeml control files and output of the one-ratio and free-ratio models; root-to-tip dN, dS and ω; PGLS results; per-site amino acid conservation. environment.yml: versions of the Python packages and command-line tools. LICENSE: license of the code. The code is released under the MIT License and the data under CC BY 4.0.