title: Standard operating procedure for computing pangenome trees.
abstract: We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family presence/absence. The weights can be chosen with emphasis on groups of gene families conserved to various degrees inside the pan-genome. The software is available for free as an R-package.
authors.forename: Lars
authors.initials: L
authors.lastname: Snipen
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery