The strict reconciliation algorithm maps the gene tree to the species tree and any incongruence is explained in terms of the minimal set of duplication and gene-loss events necessary to derive the observed gene tree topology from the one proposed in the species tree.
Briefly, this tool maps the gene list of interest to the Panther ontology and compares to the selected reference gene list to identify over- and under-represented terms.
When a list of genes is fed into IPA, its core analysis tool maps the gene list to the IPKB and generates molecular interaction networks that are most likely relevant to the input gene list.
To illustrate these factors more clearly, we generated a diagram that maps the gene duplication and loss events of the RNase gene lineages on the mammalian phylogeny (fig. 6).
Compared with the approach of Ramos et al. (2008) which creates an in silico annotation network based on pathways and protein interaction data and maps the gene list of interest afterwards, ClueGO generates a dynamical network structure by already initially considering the gene lists of interest.
