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panX: pan-genome analysis and exploration

Wei Ding, Franz Baumdicker, View ORCID ProfileRichard A. Neher
doi: https://doi.org/10.1101/072082
Wei Ding
1Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Franz Baumdicker
2Mathematisches Institut, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany
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Richard A. Neher
1Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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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 software 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 webserver or by serving panX locally as a browser-based application.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted July 18, 2017.
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panX: pan-genome analysis and exploration
Wei Ding, Franz Baumdicker, Richard A. Neher
bioRxiv 072082; doi: https://doi.org/10.1101/072082
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panX: pan-genome analysis and exploration
Wei Ding, Franz Baumdicker, Richard A. Neher
bioRxiv 072082; doi: https://doi.org/10.1101/072082

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