Gene tree/Species tree reconciliation-based orthology assignment in 28 Allorhizobium dataset

The Pantagruel pipeline was used to infer evolutionary events like gene duplication, horizontal transfer and loss, for each gene family of the 28-species pangenome with at least four sequences by reconciling the topology of gene trees with the reference species tree (core genome tree) in a probabilistic framework. Thus, genes were classified into orthologous clusters based on the gain/loss scenarios, from which clade-specific gene sets were identified. Genes specific for a particular clade (species or genus) were identified from the orthologous gene count matrix output of Pantagruel task 08, using the R script get_clade_specific_genes.r from the Pantagruel package.