Standard operating procedure for computing pangenome trees | Zendy

Lars Snipen | Zendy; David W. Ussery | Zendy

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Standard operating procedure for computing pangenome trees

Author(s) -

Lars Snipen,

David W. Ussery

Publication year - 2010

Publication title -

standards in genomic sciences

Language(s) - English

Resource type - Journals

ISSN - 1944-3277

DOI - 10.4056/sigs.38923

Subject(s) - genome , biology , gene , tree (set theory) , software , genus , software tool , computational biology , evolutionary biology , genetics , computer science , combinatorics , ecology , mathematics , programming language

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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