Hi,

I want to build a Minimum spanning tree based on cgMLST allelic profiles for e.coli isolates. I ran an analysis using pubMLST - for each genome I have a list of genes. The lists are not identical - i.e. they don't have the same number of genes (between 2500-2400 genes) How do I build a tree? What do I do for genes that are not present in all genomes?

I want to add that I tried building a tree where I just wrote N/A were an allele was gone and uploading it to PHYLOviz but I am not sure I did it OK

Any help would be appreciated Thanks