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Stand Genomic Sci. 2010 Jan 28;2(1):135-41. doi: 10.4056/sigs.38923.

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.

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