Standard operating procedure for computing pangenome trees

L. Snipen, David Ussery

    Research output: Contribution to journalJournal articleResearchpeer-review

    281 Downloads (Pure)

    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.
    Original languageEnglish
    JournalStandards in Genomic Sciences
    Volume2
    Issue number1
    Pages (from-to)135-141
    ISSN1944-3277
    DOIs
    Publication statusPublished - 2010

    Bibliographical note

    This work is licensed under a Creative Commons Attribution 3.0 License.

    Cite this