PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.

The ppanggolin msa command computes multiple sequence alignment of any partition of the pangenome. The command uses mafft with default options to perform the alignment. Please see the documentation on how parameters can be tuned for this command.