Supplemental Material for Warren et al., 2024

This file contains all of the raw orthofinder results for the analysis in <em>Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. </em>
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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)

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Please refer to the orthofinder manual for a description of files: https://github.com/davidemms/OrthoFinder#orthofinder-results-files 
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For convenience, we added a folder (<strong>GeneSymbols</strong>) 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
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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