TY - JOUR T1 - panX: pan-genome analysis and exploration JF - bioRxiv DO - 10.1101/072082 SP - 072082 AU - Wei Ding AU - Franz Baumdicker AU - Richard A. Neher Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/08/29/072082.abstract N2 - Horizontal transfer, gene loss, and gene duplication result in dynamic bacterial genomes subject to 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 for pan-genome analysis and a web-based visualization software for interactive exploration of the pan-genome. The visualization allows rapid filtering of and searching for genes. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree, and infers loss and gain of genes on the core-genome phylogeny. PanX is available at http://pangenome.de. User generated pan-genomes can be visualized either using a custom web-server or by serving panX locally as stand-alone browser-based application. ER -