Fig. 8

Programs (i.e. black letters) and corresponding effects (i.e. grew letters) implemented in the scripts ‘phyloFixedVar’, ‘GetGOxML’ and ‘EveryGO’ aiming to identify sensitive (Se) and specific (Sp) variants (SNPs and InDels) at each branches of corresponding phylogenetic inference, associate prokaryotic gene ontology (GO) terms with these homoplastic and/or non-homoplastic variants, and perform gene-ontology enrichment analysis based on the parent-child approach integrating hypergeometric tests and Bonferroni corrections, respectively. Online databases are queried by the scripts ‘GOSlimer’ and ‘GOxML’ (i.e. clouds). The GO database of the Gene Ontology Consortium is used by the script ‘GOSlimer’ to identify prokaryotic GO-terms. The QuickGO browser of the UniProt GO annotation program is queried by the script ‘GOxML’ to associate the variants with the corresponding GO-terms. These scripts were written with Python 2.7 and implement R libraries ‘p.ajust’ and ‘phyper’. The whole workflow is semi-automated (i.e. grew arrows) and the scripts ‘GetGOxML’ and ‘EveryGO’ can be performed for each variant and each branch, respectively (i.e. circular arrow)