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panX: pan-genome analysis and exploration

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Ding,  W
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Neher,  RA
Research Group Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Max Planck Society;

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Ding, W., Baumdicker, F., & Neher, R. (2018). panX: pan-genome analysis and exploration. Nucleic Acids Research (London), 46(1): e5. doi:10.1093/nar/gkx977.


Cite as: https://hdl.handle.net/21.11116/0000-000A-7D60-E
Abstract
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.