i'm also working on the Pan genome analysis of few bacterial Genomes.
I have started to use BPGA for my analysis.
It's pretty good and user friendly. It is compatible with Linux and windows as well
You need the protein.faa files as the input to the pipeline. The output has three different folders named Results, Sequences, Supporting Files.
It gives the data related to Core and Pan plots, histograms, Functional analysis like KEGG and COG pathways etc.
Feel free to ping me regarding this. Lets learn together