README This DRYAD package contains files that related to: Marianne Espeland1, Jesse Breinholt, Keith R. Willmott, Andrew D. Warren, Roger Vila, Emmanuel F.A. Toussaint, Sarah C. Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rod Eastwood, Martha A. Jarzyna, Robert Guralnick, David J. Lohman, Naomi E. Pierce, Akito Y. Kawahara (2018) A comprehensive and dated phylogenomic analysis of butterflies. This DRYAD data package will includes 12 items, including addition to this README file: Espeland_et_al_AHE_Illumina_DATA.tar.gz: Illumina anchored hybrid enrichment data in fastq format for each taxa inside a compressed (tar.gz) directory. Espeland_et_al_Butterfly_tribe_reads_only.xls: Microsoft Excel worksheet listing the Filename, sample, # trimmed paired reads, #RAW reads, sample code, and Repository. Espeland_et_al_data_alignments.tar.gz: Compressed (tar.gz) directory including 13 relaxed phylip format alignments and partition files used in analysis in Espeland et al. [13L, AA, Full_dataset, GC1, GC2, GC3, GCLE1, LE1, LE2, LE3, LE4M, PI1, PI2] Espeland_et_al_Dated_tree_Bell_2010_root_calibration.tre: Tree file in Newick format. Espeland_et_al_Dated_tree_Magallon_2015_root_calibration.tre: Tree file in Newick format. Espeland_et_al_Figure_credibility_intervals DRYAD.pdf: PDF file of the time calibrated tree with credibility intervals from Espeland et al. Espeland_et_al_NEWICK_trees.tar.gz: Compressed (tar.gz) directory including 39 phylogenetic trees estimated for Espeland et al. in newick tree format.[13L_astral.tre, 13L_astrid.tre, 13L_ML_BS.tre, AA_astral.tre, AA_astrid.tre, AA_ML_BS.tre, ALL_astral.tre, ALL_astrid.tre, ALL_ML_BS.tre, GC1_astral.tre, GC1_astrid.tre, GC1_ML_BS.tre, GC2_astral.tre, GC2_astrid.tre, GC2_ML_BS.tre, GC3_astral.tre, GC3_astrid.tre, GC3_ML_BS.tre, GCLE1_astral.tre, GCLE1_astrid.tre, GCLE1_ML_BS.tre, LE1_astral.tre, LE1_astrid.tre, LE1_ML_BS.tre, LE2_astral.tre, LE2_astrid.tre, LE2_ML_BS.tre, LE3_astral.tre, LE3_astrid.tre, LE3_ML_BS.tre, LE4M_astral.tre, LE4M_astrid.tre, LE4M_ML_BS.tre, PI1_astral.tre, PI1_astrid.tre, PI1_ML_BS.tre, PI2_astral.tre, PI2_astrid.tre, PI2_ML_BS.tre] Espeland_et_al_Alignments_used_for_BUTTERFLY1.0_probes.tar.gz: Compressed (tar.gz) directory of the alignments in fasta format used to make BUTTERFLY1.0 probe kit. Espeland_et_al_BUTTERFLY1.0_ref.tar.zip: Compressed (tar.gz) directory of the alignments in fasta format used as the reference in IBA.py (Breinholt et al 2017) for assembly of Illumina data. genome_getprobe_BLAST.py: Python script used to pull possible hits to probe loci from transcriptomes and genomes. Espeland_et_al_BUTTERFLY1.0_ProbeKit.txt: BUTTERFLY1.0 probe kit For questions regarding these data, contact Marianne Espeland [m.espeland@leibniz-zfmk.de], Jesse Breinholt at [jessebreinholt@gmail.com;jbreinholt@rapid-genomics.com] or Akito Kawahara at [kawahara@flmnh.ufl.edu].