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
