How to interpret min-hash values in phylogeny

Question

[robert.murphy]

I have generated pairwise min-hash values between 44 draft fungal genomes and am wanting to plot them into a network do display putative species and then correlate this with other methods to see if they all agree.

When generating the network I need to pick a cut off for edge values to show in the network but I am unsure how to interpret the min-hash values as a function of relatedness. It is my understanding that higher means more distant but what is a reasonable cut off value or how can I begin to determine what is?

Here is the table of pairwise min-hash values https://pastebin.com/tyEHnM6Y

The min-has values were generated with MashTree

[h.mon]

I think you will need to explore empirically and set the cut-off values yourself. Do not forget Mashtree is a fast method to get a quick tree, but it is not a model-based phylogeny reconstruction method.

[robert.murphy]

Okay thank you. Yes true, my goal is to correlate many methods to see if they all agree on the placement of the genomes. Would you advice multi locus analysis or whole genome analysis to be a better approach then (I intend to include these but can just scrap Mashtree if it is not worth using?

[h.mon]

There is no simple answer, and it boils down to understanding the biology (genome evolution), the analysis methods, and making meaningful interpretations and inferences from both.

For example: what are the biological assumptions of the "core genome" phylogeny? What are the biological assumptions of a "general genome distance" method? Are these assumptions sound, do genomes follow these assumptions? Which one fits actual genomes better? Or both fit well, but for different parts of the genomes? Same with analysis methods.

Anyway, even if Mashtree is "not worth using", it is worth reporting, as other people will have access to this information.