This README file describes the datasets used to conduct the phylogenetic analyses in the publication: An integrated phylogenetic reassessment of the parasitoid superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) results in a revised familial classification. Systematic Entomology. Authors: (1) Huayan Chen* (State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Department of Entomology, The Ohio State University, 1315 Kinnear Road, Columbus, Ohio 43212, U.S.A.) (2) Zachary Lahey* (Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, Ohio 43212, U.S.A.) (3) Elijah J. Talamas (Florida Department of Agriculture and Consumer Services, The Doyle Conner Building, 1911 SW 34th St, Gainesville, Florida 32608, U.S.A.) (4) Alejandro A. Valerio (Instituto Centroamericano para la Investigación en Biología y Conservación, P.O. Box 2398-2050 San Pedro, Montes de Oca, San José, Costa Rica) (5) Ovidiu A. Popovici (University “Al. I. Cuza” Iași, Faculty of Biology, CERNESIM, Boulevard Carol I 11, RO-700506 Iași, Romania) (6) Luciana Musetti (Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, Ohio 43212, U.S.A.) (7) Hans Klompen (Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, Ohio 43212, U.S.A.) (8) Andrew Polaszek (Department of Life Sciences, Natural History Museum, London, UK) (9) Lubomír Masner (Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada) (10) Andrew D. Austin (Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, Australia) (11) Norman F. Johnson (Martha N. and John C. Moser Chair in Arthropod Biosystematics and Biological Diversity, Department of Evolution, Ecology and Organismal Biology and Department of Entomology, The Ohio State University, 1315 Kinnear Road, Columbus, Ohio 43212, U.S.A.) * These authors contributed equally. ================================================================================================================= Correspondence for this README: Zachary Lahey (lahey.18@osu.edu) ================================================================================================================= Computer software required to reproduce analyses: MAFFT for multiple sequence alignment (MSA; https://mafft.cbrc.jp/alignment/software/); IQ-TREE (http://www.iqtree.org/) to conduct phylogenetic analyses on MSAs produced with MAFFT. ================================================================================================================= Files: The single tarball file (chen_et_al_2021_analyses.tar.gz) contains two directories, one for the 4 gene sanger sequencing analysis and one for the phylogenomic analysis of basal taxa. ================================================================================================================= Contents of directories and subdirectories: (1) 4_gene_platy A. molecular_SITE: this subdirectory includes the following files -- the concatenated nucleotide alignment (Platy_all_concatenated_20180711.phy), partition file (platy_all_molecular_partitions.nex), bash script with command to run IQ-TREE (run_platy_all_molecular_part_bnni_SITE_no_encyrto.sh), and IQ-TREE output files (remaining files in this directory). B. morphomolecular_SITE: this subdirectory includes the following files -- the concatenated nucleotide alignment (Platy_all_concatenated_20180711.phy), morphological character codings for each taxon in the concatenated nucleotide alignment (platy_morpho.phy), partition file (platy_all_morphomolecular_partitions.nex), bash script with command to run IQ-TREE (run_platy_all_morphomolecular_part_bnni_SITE_no_encyrto.sh), and IQ-TREE output files (remaining files in this directory). (2) phylogenomics_platy A. 13taxa: this subdirectory includes the following files -- the concatenated amino acid alignment (13taxa.fasta), partition file (13taxa_modelfind.best_scheme.nex), bash script with command to run IQ-TREE (iqtree_13taxa_modelfind_bnni_SITE.sh), and IQ-TREE output files (remaining files in this directory, excluding those in the modelfinder subdirectory). i. modelfinder: this subdirectory includes the following files: the concatenated amino acid alignment (13taxa.fasta), partition file (13taxa.part), bash script with command to run IQ-TREE (iqtree_13taxa_modelfind.sh), and IQ-TREE output files (remaining files in this directory). * Note that the bash scripts (.sh files) included in each of these directories cannot be run as-is. The user will need to modify their $PATH depending on where IQ-TREE is installed on their computer. The reader is referred to the IQ-TREE webpage (http://www.iqtree.org/doc/Home) for details on what each of the IQ-TREE output files contain.