Supplementary Data for: MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

Orthogroups, species tree and the MicroFinder protein set Files listed below are found in the "./OrthoFinder_results_and_MicroFinder_protein_set/" subdirectory. Sample IDs used throughout correspond to those given in Supplementarty Table 1 of the main manuscript. SubdIrectory containing proteomes for each species included in the OrthoFinder analysis: ./input_proteomes/ SubdIrectory containing annotation GFF files for each species included in the OrthoFinder analysis: ./annotations/ OrthoFinder orthogroups: Orthogroups.txt Per species gene counts per orthogroup annotated with whether each familiy was identied by KinFin as a broadly conserved "fuzzy" orothogroup and whether the orthogroup was included in the MicroFinder protein set: Orthogroups.GeneCount.KinFin_MicroFinder_annotated.tsv SubdIrectory containing multiple sequence alignments for all orthogroups: ./MultipleSequenceAlignments_all_orthogroups/ SubdIrectory containing multiple sequence alignments for conserved single copy orthogroups used for IQTree species tree inference (FASTA headers have been simplified to just contain the species ID): ./species_tree_alignments/ IQtree species tree inference run details: species_tree.concat.iqtree IQtree species tree: species_tree.concat.nwk IQTree best fitting models and parititioning scheme: IQTree.concat.best_model.nex The MicroFinder protein set used in the MicroFinder pipeline: MicroFinder_prot_set.fa Re-curated bird genomes The "./Recuration/" subdirectory contains files used for the MicroFinder-enabled genome assembly curation of 12 previously released bird genomes listed in Supplementary Table 4 of the main manuscript. Subfolders in this directory are named by the TOL ID of each species and contain: PretextView HI-C contact map of the original genome assembly. PretextView savestate showing changes made during re-curation. AGP file summarising changes made to the orginal assembly. Updated genome assembly FASTA file.