README panoat orthogroups 30/08/2023

Orthogroups were identified using orthofinder 2.5.5 (https://doi.org/10.1186/s13059-019-1832-y). Instead of “standard” orthogroups so called HOGs (Phylogenetic Hierarchical Orthogroups) are reported which are orthogroups inferred at each node in the species tree (see https://github.com/davidemms/OrthoFinder#phylogenetic-hierarchical-orthogroups-directory). Genomes were split into individual subgenomes (A-C-D, A-B, C-D) and therefore one HOG at species level contains at least 3 genes in 1:1:1 or N:N:N ratio. 

File format is tab delimited with the following format:
“HOGID” “OGID” “Gene Tree Parent Clade” “Species1…SpeciesN

“panoat.orthologs.all_split_subgenomes.N0.Aug2023.tsv” -> contains the orthogroups for genotypes 
“panoat.orthologs.split_subgenomes_expression_data.N0.Aug2023.tsv” -> orthogroups for all genotypes with expression data

