Supporting Information for: Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

<p>This data repository contains supporting information, data, and code for figures and analysis pipelines the PLOS Biology article: "Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life."</p> <ul> <li><strong>4d_full.treefile</strong>: Data underlying Figure 1 (note: tree was plotted as a cladogram and key groups collapsed on iToL; the treefile was not modified) and Figure S1.</li> <li><strong>S2_data.csv</strong>: Data underlying Figure 2.</li> <li><strong>S3_data.csv</strong>: Data underlying Figure 3.</li> <li>Data underlying Figure 4 is found in Table S4 of supplementary_tables.xlsx in the main manuscript</li> <li><strong>S5_data.csv</strong> Data underlying Figure 5</li> <li><strong>S6_data.csv</strong> Data underlying Figure S2&nbsp;</li> <li><strong>illumina_only_assms.tar.gz</strong>: Archive of Illumina-only assemblies (FASTA) based on publicy available data that we did not generate. Assemblies generated from our own short-read data have been submitted to NCBI GenBank.</li> <li><strong>illumina_vcfs.tar.gz</strong>: Illumina-based variant calls and BED tracks of masked bases.</li> <li><strong>genomes.tar.gz</strong>: Genome files, for archival purposes.</li> <li><strong>repeatModeler-lib.tar.gz</strong>: RepeatModeler2 libraries.</li> <li><strong>diploid_genomes.tar.gz</strong>: diploid genomes and BED tracks of phased regions.</li> <li><strong>trees.tar.gz</strong>: phylogenies</li> </ul>