### Data supplementing the article "De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in the fungal genus Amanita" This repository contains the following files: 1. Scripts The script is not usable immediately, needs adapting - RAxML.sh pipeline for phylogenetic reconstruction - HGT -- AUtest.sh: pipeline to run AU test - duplication -- OrthologDetect.py: pipeline to detect orthologs -- EcMparalogDectect.R: pipeline to detect EcM-paralogs -- hyphyabsrel.sh: pipeline to test for positive selection 2. Analysis results - FastOrtho: end file for FastOrtho using 1.5 as inflation value - dNdS: CDS alignments from PRANK for estimating dN/dS with PAML - denovo: alignment between de novo genes and their putatively homologous non-coding region - HGT: alignments and phylogenies of HGT family - duplication: alignment, phylogeny of duplication family and subset for Absrel analyis