Thanks for sharing!

You can consider adding your packages to http://packagedata.net/

Are you familiar with this other phylogenetics package? https://github.com/IstvanZachar/Phylogenetics

Finally, may I suggest converting it to a true package (following the standard structure, having its own context, etc.)? You will find many resources on getting started here: https://mathematica.stackexchange.com/a/132960/12

Once you are confident creating packages that follow the standard structure, you can consider distributing them as paclets: https://mathematica.stackexchange.com/q/131101/12 This provides a robust, user-friendly installation and uninstallation method.

A new version of Phylogenetics for Mathematica (v6.2) is available, along with user guide. The package now has more tree manipulation functions, phylogenetic comparative methods, implementation of Gene Hunt's evolutionary model fitting routines for stratigraphic sequences.

My packages Geometric Morphometrics for Mathematica, Quantitative Paleontology for Mathematica, and Modularity for Mathematica (with Anjali Goswami) are available on the same page.

The following graphic was produced using the MapTraitsOntoTree function from the Phylogenetics pacakge.

Thank you! I used your package some years ago and was very useful. We recently released the Function Repository. Maybe you can consider submitting it there?

The function repository accepts single functions. How would a package, which contains many inter-dependent functions, fit there?

I'm eagerly waiting for the paclet repo!

Does the function repository allow dependence on other function repository functions?

There is now a phylogenetic tree plotting function in the Wolfram Function Repository.

https://resources.wolframcloud.com/FunctionRepository/resources/PhylogeneticTreePlot

It uses a particular method, and with hard-wired parameter values. So there is no flexibility for tuning. But of course the code is available in the author notebook in case people want to make alterations. Also I'd be curious to learn about experiments with different methods.

The structure of your tree tree is more complicated than my code expects. In addition to tips and branch lengths, your file has entries for node names. For example, one bit of the tree file looks like this:

(Belgium/ULG-6216/2020:0.03161716056206387,Ireland/Dublin-19072/2020:0.0015625157534486789)NODE_ 0000305:0.00780043233021388

That treats "Belgium/ULG-6216/2020" and "Ireland/Dublin-19072/2020" as two tips, each with a branch length after their respective ":". They are then enclosed in parentheses. What follows "NODE_0000305" appears to be a node label followed by ":" and the subtending branch length. My code is vomiting on the node name because it expects a ":" directly after the closing parenthesis (my code automatically numbers nodes using its own scheme).

You could probably strip out the node names with a search and replace for "NODE*:" to ":" if you have the right tool. Even Word will do it with the right wildcard options.

Warning though, my function is not terribly efficient. It's performance may not be great with trees this big, so expect it to be a little sluggish.