ABSTRACT
The Genome Biology website, which can be accessed via the National Center for Biotechnical Information (NCBI) home page, offers several resources by which various genomes can be analyzed. The overlap of genes from two or more genomes can be visualized by use of Venn diagrams or programs such as EDGAR and Sungear. Identified orthologs of genes across multiple species can be grouped into clusters of orthologous groups (COGs). Single linkage clustering compares genes in a cross-species context, based only upon sequence, and allows the construction of a presence/absence matrix. Genome content analysis was first demonstrated for bacterial genomes and can now be performed by computer software packages and has been extended to include many eukaryotes. Pangenomes have become an important tool in phylogenomics. In this chapter we examine various programs that are useful in pangenome analysis.
