Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance

Scripts and files associated with "Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance". Specific details are below:
ERC analyses - Trees and script used to perform ERC analyses
PPI analyses - Files and scripts used to perform PPI analyses. For size reasons, output docking scores are only provided.
Gene expression analyses - Files and scripts associated with gene expression analyses. For size and path reasons, raw salmon counts and filtering are not included. 
Nuclear OXPHOS alignments tree - Individual protein alignments and a concatenated alignment of all proteins. Phylogenetic reconstruction files are also provided
Transcriptome assemblies - All transcriptome assemblies generated in this study. Included files are QC statistics, the raw transriptome assembly, and the final assembly deposit on the NCBI TSA.