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Nucleic Acids Res. 2018 Jan 9;46(1):e5. doi: 10.1093/nar/gkx977.

panX: pan-genome analysis and exploration.

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Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
Mathematisches Institut, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany.
Biozentrum and SIB Swiss Institute of Bioinformatics, University of Basel, 4056 Basel, Switzerland.


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 Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.

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