Evolutionary history of the Hymenoptera - Supplementary Datasets
Data deposited for the paper: Evolutionary history of the Hymenoptera 1) Folder name: 1-Gene-MSAs_after-pal2nal Kind of data: Multiple sequence alignments of orthologous genes after alignment refinement (aa and nt data). 2) Folder name: 2-Main-dataset_dataBlocks-PartitionfinderResults-Final-supermatrix Kind of data and file formats: • Main data set: Concatenated supermatrices after the Aliscore and Mare step. Sites have been rearranged according to clan, Pfam-A, Pfam-B and void data blocks. Files are in phylip format. • Corresponding data block files are given as text files. Data blocks and the supermatices are used as input for the PartitionFinder analysis. • Results of the PartitionFinder analysis: Best partitioning scheme in RAxML partition file format. • Files that contain the word “reduced” in their name are the alignment and partition file produced by RAxML when automatically filtering alignment sites, which contain only gap and ambiguous characters. • All above files are given for aa and nt data sets. 3) Folder name: 3-datasets_decisive-datasets Kind of data and file formats: As in number 2) but for the data sets reduced to the decisive data sets. That is, data blocks with missing data in required taxonomic groups has been removed. Decisive data sets are: Aculeata-decisive-dataset, Apoidea-decisive-dataset, Backbone-decisive-dataset. 4) Folder name: 4-datasets_FCLM_and_permutations Kind of data and file formats: Data sets used for the Four Cluster Likelihood Mapping method. Files include the partition files in RAxML Format, the taxonomic group files as well as the necessary data sets from which the permutations have been generated. For detail on the methods and the purpose of the permutation test see the Supplemental Experimental Procedures (available online). The generating scripts for the permuted data sets are available upon request. Permuted data sets can also be created by following the description in the Supplemental Experimental Procedures. The reduced matrix is the matrix that was used as input in the permutation script. 5) Folder name: 5-results_rogue_taxa_analyses Kind of data and file formats: Result files of the program RogueNaRok for different parameters. Results are given for the analyses conducted for the aa and the nt data sets. 6) Folder name: 6-results_tree_reconstruction_decisive_datasets Kind of data and file formats: Resulting phylogenetic trees in Newick format for the decisive data sets. 7) Folder name: 7-results_FCLM_and_permutations Kind of data and file formats: Result files of the FCLM analysis. Files are graphic files in the SVG format. 8) Folder name: 8-results_tree-reconstruction_main_analysis Kind of data and file formats: Resulting phylogenetic trees in Newick format of the main analysis. 9) Folder name: 9-dating_dataset_and_results Kind of data and file formats: Input and result files of the dating analysis.