  Motivation: The gene content regulates the biology of an organism. It varies
between species and between individuals of the same species. Although tools
have been developed to identify gene content changes in bacterial genomes, none
is applicable to collections of large eukaryotic genomes such as the human
pangenome.
  Results: We developed pangene, a computational tool to identify gene
orientation, gene order and gene copy-number changes in a collection of
genomes. Pangene aligns a set of input protein sequences to the genomes,
resolves redundancies between protein sequences and constructs a gene graph
with each genome represented as a walk in the graph. It additionally finds
subgraphs, which we call bibubbles, that capture gene content changes. Applied
to the human pangenome, pangene identifies known gene-level variations and
reveals complex haplotypes that are not well studied before. Pangene also works
with high-quality bacterial pangenome and reports similar numbers of core and
accessory genes in comparison to existing tools.
  Availability and implementation: Source code at
https://github.com/lh3/pangene; pre-built pangene graphs can be downloaded from
https://zenodo.org/records/8118576 and visualized at
https://pangene.bioinweb.org
