Data from: Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming

Supplementary data to the research article: <br> <b>Phylogenomic analyses clarify the pattern of evolution</b><b> of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming</b> <br> Authors: Alexandros Vasilikopoulos, Michael Balke, Sandra Kukowka, James M. Pflug, Sebastian Martin, Karen Meusemann, Lars Hendrich, Christoph Mayer, David R. Maddison, Oliver Niehuis, Rolf G. Beutel, Bernhard Misof <br> The following directories are included: <br> <b>01.Ortholog_set</b> Description: Ortholog set used for bait design in this study (the format is intended for use in the software package Orthograph) <br> <b>02.Bait_sequences</b> DescriptionThis folder includes (a) the file with the bait nucleotide sequences, (b) a dictionary of the gene IDs of <i>Tribolium castaneum</i> and corresponding OrthoDB IDs of genes used for target enrichment and (c) a file with the IDs of the targeted exons (based on annotation of <i>T. castaneum</i> v. 5.2 in the form GENEID_X_Y, where X: the number of exon targeted and Y: the total number of exons for that gene) <br> <b>03.Clean_assemblies_hybrid_enrichment_data</b> Description: Assemblies of the hybrid-enrichment genomic data after removal of putative cross-contaminations <br> <b>04.Alignments_before_Aliscore</b> Description: Amino-acid and nucleotide alignments before trimming with Aliscore <br> <b>05.Supermatrices</b> Description: All inferred and analyzed supermatrices <br> <b>06.Treefiles_supermatrices</b> Description: All phylogenetic trees inferred from analyses of supermatrices (best trees for maximum likelihood analyses) <br> <b>07.Filtered_datasets_coalescent_analyses</b> Description: All analyzed amino-acid alignments used in summary coalescent phylogenetic analyses (filtered alignments) <br> <b>08.Gene trees_non-collapsed</b> Description: All inferred gene trees used as input in summary coalescent analyses (before collapsing weakly supported nodes) <br> <b>09.Treefiles_coalescent_analyses</b> Description: All inferred species trees resulted from summary coalescent phylogenetic analyses <br> <b>10.Custom_scripts</b> Description: Custom scripts used in the study<br><br>