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Verts_teleosts_fasttree_orthofinder.tar.gz (1.48 GB)

Supplemental Material for Warren et al., 2024

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posted on 2024-05-16, 14:26 authored by Wesley C. Warren, Edward S. Rice, Maggs X, Emma Roback, Alex Keene, Fergal Martin, Denye Ogeh, Leanne Haggerty, Rachel A. Carroll, Suzanne McGaugh, Nicolas Rohner

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

History

Article title

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

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