Standard operating procedure for computing pangenome trees

L. Snipen, David Ussery

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    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.
    Original languageEnglish
    JournalStandards in Genomic Sciences
    Issue number1
    Pages (from-to)135-141
    Publication statusPublished - 2010

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