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:
Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming
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
The following directories are included:
01.Ortholog_set
Description:
Ortholog set used for bait design in this study (the format is intended for use in the software package Orthograph)
02.Bait_sequences
Description
This folder includes (a) the file with the bait nucleotide sequences, (b) a dictionary of the gene IDs of Tribolium castaneum 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 T. castaneum 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)
03.Clean_assemblies_hybrid_enrichment_data
Description:
Assemblies of the hybrid-enrichment genomic data after removal of putative cross-contaminations
04.Alignments_before_Aliscore
Description:
Amino-acid and nucleotide alignments before trimming with Aliscore
05.Supermatrices
Description:
All inferred and analyzed supermatrices
06.Treefiles_supermatrices
Description:
All phylogenetic trees inferred from analyses of supermatrices (best trees for maximum likelihood analyses)
07.Filtered_datasets_coalescent_analyses
Description:
All analyzed amino-acid alignments used in summary coalescent phylogenetic analyses (filtered alignments)
08.Gene trees_non-collapsed
Description:
All inferred gene trees used as input in summary coalescent analyses (before collapsing weakly supported nodes)
09.Treefiles_coalescent_analyses
Description:
All inferred species trees resulted from summary coalescent phylogenetic analyses
10.Custom_scripts
Description:
Custom scripts used in the study
