Input: NCBI GenBank records or user's own genome sequences in GenBank format

Clustering: DIAMOND + MCL + phylogeny-based post-processing


Fig.1 An overview of pan-genome analysis and visualization pipeline.

PanX analysis pipeline is based on DIAMOND, MCL and phylogeny-aware post-processing to determine clusters of orthologous genes from a collection of annotated genomes. PanX generates a strain/species tree based on core genome SNPs and a gene tree for each gene cluster.

PanX interactive visualization:

(1) The dynamic pan-genome statistical charts allow rapid filtering and selection of gene subsets in the gene cluster table;

clicking a gene cluster in the cluster table loads (2) corresponding alignment, (3) individual gene tree and (4) gene presence/absence and gain/loss pattern on strain/species tree;

(5) Selecting sequences in alignment highlights associated strains on strain/species tree;

(6) (7) Strain/species tree interacts with gene tree in various ways;

(8) Zooming into a clade on strain/species tree screens strains in metadata table;

(9) Searching in metadata table display strains associated with specific meta-information.