Supplemental Material for Warren et al., 2024

This file contains all of the raw orthofinder results for the analysis in Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. The dataset includes: Orthogroup sequences Single copy orthologue sequences Multiple sequence alignments Species Trees Putative Xenologs Phylogenetic hierarchical orthogroups Resolved gene trees Gene duplication events Reports on comparative genomic statistics Assignments of genes to orthogroups Reports of pairwise orthologues Gene trees Gene Symbol Assignment (GeneSymbols folder) Please refer to the orthofinder manual for a description of files: https://github.com/davidemms/OrthoFinder#orthofinder-results-files For convenience, we added a folder (GeneSymbols) with gene symbols assigned to stable ids per orthogroup. This contains one tab delimited file per orthogroup. Each file contains the gene symbols assigned to each stable id, based on the annotations used as input. The format is: annotationfile:stable-id genesymbol gene description speciescode The species code is Ciona intestinalis=Cint Monodelphis_domestica=Mdom Pan_troglodytes=Ptro Rattus_norvegicus=Rnor Xenopus_tropicalis=Xtro Podarcis_muralis=Pmur Oryzias_latipes=Olat Mus_musculus=Mmus Lepisosteus_oculatus=Locu Homo_sapiens=Hsap Gallus_gallus=Ggal Danio_rerio=Drer Astyanax_mexicanus=Amex Xiphophorus_maculatus=Xmac Pseudonaja_textilis=Ptex