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. 2021 Sep 24;7(9):000670. doi: 10.1099/mgen.0.000670

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© 2021 The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

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Fig. 1. — Twilight pan-genome analysis workflow. (a) A collection of genomes are grouped into lineages of closely related isolates. (b) Each gene is classified as core, intermediate or rare in each lineage, depending on its frequency within the lineage (as defined in the grey box). (c) The classification of the entire gene pool across all lineages consists of a total of 13 distribution classes. These include the number of lineages in which a gene is present (all lineages, multiple lineages or a single lineage), and the combination of frequency assignments of the gene in those lineages (core, intermediate or rare).