Fig. 11

Case study: Difference between GFC cluster and YGOB pillars - Phylogenetic analysis. a displays a portion of 6 YGOB pillars, where we are interested in the two pillars (red and blue columns). YGOB classifies them as separate clusters as shown in (a) but GFC-Single and GFC-Average classifies Ecym_1340 to be part of blue pillar and AEL037C to be a singleton gene. a also shows that both the cluster and the pillar has good syntenic support via neighboring pillars. b displays the D/L score and the most parsimonious reconciliation of gene tree with species tree constructed from GFC cluster with/without Ecym_1340 added and highlighted here in blue. The cluster given by GFC-based methods (Ecym_1340 added to the blue cluster in a) has the lowest D/L score to gene ratio and is, therefore, phylogenetically most probable. There exist multiple genes in the blue pillar that have a BLAST hit with Ecym_1340 and there does not exist a BLAST hit with evalue 10 between Ecym_1340 and AEL037C showing similarity support for GFC cluster and lack of similarity for the genes in red pillar in (a)