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Tree parsing

Tree rooting


Speciation/duplication detection

Duplications and speciations were mapped using the species overlap algorithm as implemented in the Environment for Tree Exploration program (ETE)

The species-overlap algorithm is an alternative approach of inferring evolutionary events from gene phylogenies. The only evolutionary information required by such algorithm is a rooted gene tree. This method requires neither a fully-resolved species phylogeny, nor reconciliation steps. To decide whether a given node represents a speciation or a duplication event, this algorithm employs the level of overlap between species represented under its two descendant nodes. In brief, a species-overlap score (SOS) is calculated for every node as the proportion of shared species between child branches over the total number of organisms under the node. If the SOS is higher than given threshold, the parental node is mapped as duplication, otherwise as speciation event. The best performance of the algorithm has been reported to be associated with the use of a SOS threshold equal to 0.0, so speciation is only assumed if no species overlap is detected between its descendant nodes. 

Dealing with multifurcations


In addition, Maximum likelihood trees for orhtologous groups from OrthoMCL have been reconstructed using PhylomeDB pipeline (PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome[PMID: 24275491]).