Screenshot of a reconciled phylogenetic tree displayed with ETE. The image shows a portion of a reconciled tree generated using the ETE's strict reconciliation algorithm over an example gene phylogeny. The most accepted tree of life for the species considered was used for reconciliation. A custom ETE layout function has been used to highlight different aspects of the tree: Grey dashed lines represent the inferred gene losses. Blue nodes indicate duplication events. Red nodes represent speciation events. Each OTU is displayed with their corresponding name and species image. Part of the multiple sequence alignment is displayed with each sequence associated to its corresponding OTU.