I’ve been spending a lot of time lately speculating about the phylogeny of cynipid wasps. I’d love to be able to organize my thoughts with some kind of tool that allows me to conveniently draw and edit a tree, append various kinds of secondary information, view it different ways, etc. Someone recomm…

I think most phylogeny programs are built around generating a tree from some sort of data. This is kind of tongue-in-cheek, but what programs do people use to draw tournament brackets? If you work out from the final match instead of inwards, those are basically neighbor-joining trees…

I don’t know of any programs that let you manually draw a tree (the editing features of Mesquite are the closest I can think of), but if you become comfortable writing out the structure of trees in Newick Notation (which, admittedly, can be extremely cumbersome if you have a lot of taxa) you can vis…

The one I made in Mesquite looks like this. It has a lot of tiny annoyances that add up. Eg the font size is stuck small, every time you scroll all the text flashes, it’s very awkward to save a tree, no way to collapse clades, etc. It’s just not a very user-friendly experience. [example2]

so you’re just looking for bigger fonts and the ability to collapse / prune nodes?

I mean Mesquite is technically capable of doing what I want to do, it’s just very unpleasant to use, and fixing those issues would ameloriate some of my bigger complaints. But I don’t know that Mesquite is the sort of thing that can just be easily changed. Eg the font size thing I looked up and foun…

Wikipedia has a page dedicated to this very question: List of phylogenetic tree visualization software I haven’t used any of them, so I can’t recommend one over the other, but there are a bunch of options both on and offline, free and premium. I’d look at the open-source desktop applications as …

If you already have a file in a tree data format I would just upload it to iTOL and use that - https://itol.embl.de/ . Maybe you could save your Mesquite tree into a newick format or something similar and upload it to one of these other suggested tools that has an editing interface you prefer. If you…

[image] Megachile: It’s just not a very user-friendly experience Welcome to Mesquite. It’s powerful in that it lets you go from start to finish on a project, but it is frustrating because of its baked-in limitations and old-fashioned interface. R packages are also super powerful but frustrat…

Echoing what others have said, I build the custom topology in Mesquite, then export and make it look nice in Figtree.

Recommend programs for editing phylogenetic trees?

Nature Talk

pisum June 29, 2022, 1:04am 4

what does the output of Mesquite look like? and what kind of edits are you thinking of making?

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Recommend programs for editing phylogenetic trees?

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