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Background  The term  pan-genome  was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently.    Results  This work focuses on providing a tool for discovering and visualizing the relationships between the sequences constituting a pan-genome. A new structure to represent such relationships – called  affinity tree  – is proposed. Each node of this tree has assigned a subset of genomes, as well as their homogeneity level and averaged  consensus sequence . Moreover, subsets assigned to sibling nodes form a partition of the genomes assigned to their parent.    Conclusions  Functionality of affinity tree is demonstrated on simulated data and on the  Ebola virus  pan-genome. Furthermore, two software packages are provided:  PangTreeBuild  constructs affinity tree, while  PangTreeVis  presents its result.

Getting insight into the pan-genome structure with PangTree