Pan-genome analysis of eukaryotes has become more common, but many of the available software for pan-genome analysis are intended for use with prokaryote data, developed Pangloss, a pipeline that allows users to generate input data and construct species pan-genomes for microbial eukaryotes using the synteny-dependent PanOCT method and various downstream characterisation analyses.

Large number of available bacterial genomes makes Pan-genome analysis more meanful, many fungal species have no enough genomes for reliable analysis. Some estimations show that we need from 15 to 30 genomes