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

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."

4d_full.treefile: 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.

S2_data.csv: Data underlying Figure 2.

S3_data.csv: Data underlying Figure 3.

Data underlying Figure 4 is found in Table S4 of supplementary_tables.xlsx in the main manuscript

S5_data.csv Data underlying Figure 5

S6_data.csv Data underlying Figure S2 

illumina_only_assms.tar.gz: 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.

illumina_vcfs.tar.gz: Illumina-based variant calls and BED tracks of masked bases.

genomes.tar.gz: Genome files, for archival purposes.

repeatModeler-lib.tar.gz: RepeatModeler2 libraries.

diploid_genomes.tar.gz: diploid genomes and BED tracks of phased regions.

trees.tar.gz: phylogenies