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Phylogenetic Pangenome Accumulation - v1.4.0
By: dylan


View a Pangenome in a phylogenetic context.

View a Pangenome in a phylogenetic context. Allows the dissection of Pangenome categories using the Species Tree so that one can determine when gene families entered or left a branch of interest.

Pangenome Categories

A Pangenome is the set of all genes found in a collection of related organisms, typically members of a species clade, which are then grouped or associated by sequence homology across species. Some methods that determine pangenomes, such as OrthoMCL, attempt to distinguish which homologous genes are true orthologs and vertically inherited from those with lineage derived paralogous expansions by duplication.

Orthologous gene sets within a pangenome are typically partitioned into three categories: Core, Singleton, and the remaining ortholog sets just considered the rest of the Pangenome (here termed the Partial Pangenome ).


Pangenome: The pre-calculated pangenome object (containing the orthology relationships between the genes) to use for the visualization. Only one Pangenome object can be used.

Species Tree: The phylogenetic pangenome accumulation is determined within the context of the Species Tree. Unless you select the skip missing genomes option, every Genome in the Species Tree must be contained within the Pangenome object (but not every Genome in the Pangenome object needs to be in the Species Tree). The same Narrative must be used for the Genomes found in the Pangenome and the Species Tree. Additionally, the user may choose to require that the versions of the Genome objects that were included in the Species Tree and the Pangenome must match with the Enforce Genome version match option. Only one species Tree can be used at a time.

Save Pangenome feature sets: Feature Sets containing Core, Singleton, and Partial Pangenome (see above) gene members from the ortholog clusters are created if this option is set. These categories are calculated and generated for each node in the Species Tree, using the collection of genomes for which that node represents the ancestor (i.e. the leaves of that branch).

Team members who developed & deployed algorithm in KBase: Dylan Chivian. Species Tree Builder by Roman Sutormin and Paramvir Dehal. For questions, please contact us.

Related Publications

App Specification:

Module Commit: aed8564fcf4c6e8a3e94f6546715496e6fffbd84