Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species

All data are stored in separate .tar.gz archives, each corresponding to a single species. Each archive contains four files: (i) predicted protein sequences including all isoforms, (ii) predicted protein sequences containing only the longest isoform per gene, (iii) a structural annotation file, and (iv) a structural annotation file decorated with Gene Ontology terms in .gff3 format. For example, Drosophila_melanogaster.tar.gz contains Drosophila_melanogaster.faa, Drosophila_melanogaster_longest.faa, Drosophila_melanogaster.gtf, Drosophila_melanogaster.gff3, and Drosophila_melanogaster_interproscan.tsv.Additionally, for user convenience, the structural annotation files decorated with Gene Ontology terms files (.gff3) have also been uploaded separately to allow quick access. This results in duplication, as the .gff3 files are available both individually and within the respective species archives.The results of the OrthoFinder2 analysis have been provided as a separate archive, OrthoFinder2_Results.tar.gz.In addition, the protein multiple sequence alignment used to reconstruct the species phylogeny has been included. A species tree was inferred using <b>RAxML-NG</b> with the <b>LG+G8+F</b> substitution model. The following files are provided in the OrthoFinder2 results:<code>200_insects_raxml.pdf</code> – visual representation of the tree<code>200_insects_raxml.nwk</code> – Newick-format tree file<code>SpeciesTreeAlignment.fa</code> – protein multiple sequence alignment used for tree inference<br>The genome sequences used as input for these annotations were obtained from NCBI. Details of the corresponding accession numbers, the specific BRAKER version used and whether the genomes had prior annotations could be found in README.txt file in this repository.<br><br>