Files used for analyses in the article "Genomic identification of Wolbachia reveals widespread signals of codivergence in a butterfly subfamily (Hesperiidae: Eudaminae)"

All_loci_consensus_sequences_v2.fasta 406 curated nuclear butterfly protein coding genes (PCGs) used in the SECAPR pipeline for the extraction, from every studied butterfly specimen, of the contigs containing these PCGs. 406_butterflyNuclearPCG.fasta.tar.gz Individual FASTA files of the 406 PCGs, used for the obtention of exonic regions from the contigs of every studied butterfly specimen. superARefGenes.fasta 124 curated Wolbachia genes used in the SECAPR pipeline for extraction of loci from Wolbachia assembled contigs for supergroup A. The genes in this file were adapted in our study, but they were originally published in Wang et al., 2020 (https://doi.org/10.1093/gbe/evaa219) superBRefGenes.fasta 124 curated Wolbachia genes used in the SECAPR pipeline for extraction of loci from Wolbachia assembled contigs for supergroup A. The genes in this file were adapted in our study, but they were originally published in Wang et al., 2020 (https://doi.org/10.1093/gbe/evaa219) 124WolbLociFASTAs.tar.gz Individual FASTA files of the 124 Wolbachia loci used for the obtention of exonic regions from the contigs of every studied butterfly specimen. 124lociWolb.phy Final concatenated alignment of Wolbachia extracted loci used for the phylogenetic inference of the Wolbachia supergroups infecting our studied samples. ButterflyConcatenated.phy Final concatenated alignment of butterfly extracted PCGs used for the phylogenetic inference of the butterfly species. wolbBlastXSuperA.tar.gz Results from the BLASTX search analysis used to identify Wolbachia supergroup A proteins in the studied specimens' contigs. The results are in TSV format, and the files are the "raw", non-filtered tables directly resulting from the BLASTX analyses. These tables were filtered as described in Methods. wolbBlastXSuperB.tar.gz Results from the BLASTX search analysis used to identify Wolbachia supergroup B proteins in the studied specimens' contigs. The results are in TSV format, and the files are the "raw", non-filtered tables directly resulting from the BLASTX analyses. These tables were filtered as described in Methods. cecropterusBlastNTSVs.tar.gz Results from the BLASTN searches used especifically in Cecropterus dorantes samples that contained biased Wolbachia identification. speciesButtTree.treefile Tree file obtained with IQTree 2 for the butterfly protein coding loci phylogenetic tree. 124WolbLoci.treefile Tree file obtained with IQTree 2 for the Wolbachia loci phylogenetic tree. partitionsButterfly.best_model.nex Best evolutionary models found for the inference of the butterfly species' phylogenetic tree. partitionsWolb.best_model.nex Best evolutionary models found for the inference of the Wolbachia supergroups' phylogenetic tree. command_Line_Scripts.txt Main scripts/commands used for Wolachia identification and phylogenetic analysis. R_scripts.txt R scripts used for matrix obtention, mantel tests, PACo, GLM and heatmaps.