Charley G. P. McCarthy & David A. Fitzpatrick (2019). Pangloss: a tool for pan-genome analysis of microbial eukaryotes. Genes, 10(7):521. Link.
Pangloss is a pipeline intended primarily for performing pan-genome analysis of microbial eukaryotes such as yeasts and other fungi. Pangloss can perform gene prediction using up to three different prediction methods, pan-genome construction using PanOCT and a bunch of downstream functional annotation analyses and data visualization analyses. For the full range of stuff that Pangloss can do, a walkthrough of how to run Pangloss and information on how to install various dependencies Pangloss needs to run - see the included manual.
Any bugs or problems feel free to email me at Charley (dot) McCarthy (at) mu (dot) ie, or raise an issue here on the repo.