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 recommended Mesquite for this purpose and while it is technically capable of doing what I want, I found it extremely cumbersome to use, to the point that it wasn’t really worth it. I’m hoping that I can find something more user-friendly. Does anyone have any recommendations?
To be clear I’m looking for something I can manually edit, not something that will generate trees for me from DNA or other information. This is part of the problem with Mesquite–it seems designed around generating trees from stored data with a minimal role for manual editing.
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 visualize the trees with tools like Figtree (this is what I use) or TreeViewer (it has some really nice features and user interface but always crashes on my computer - maybe you will be more lucky). If you like coding you can make some really nice figures in R with ggtree or phytools but it has a steeper learning curve.
In Mesquite it has features to generate the tree from data, but you can also upload a starting tree (written in Newick notation) and then edit it from there.
what does the output of Mesquite look like? and what kind of edits are you thinking of making?
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.
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 found an old github issue and the developers seemed to imply they thought there was nothing they could do about it.
Wikipedia has a page dedicated to this very question:
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 those will be free and not limited to online use. You’ll have to look through the descriptions to decide with is at the appropriate ease of use level. Some of them are pretty simple, others are really technical:
And, of course R has packages and tutorials for creating and editing phylogenetic trees:
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 are just trying to draw a cladogram and dont actually have any data other than knowing the relationships I’m not really sure, you might just want to use illustrator or powerpoint to draw it.
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 frustrating. The advantage there is that you can usually eventually get it to do what you want… if you learn your coding.
I’ll second @elsemikkelsen in recommending FigTree. I’ve found it makes the prettiest trees for the least amount of work, and it’s free. The only issue is that you just can’t rearrange your topology within the program. I make trees in other software (because they’re being estimated from a dataset) or by manually editing the Newick file (when I’m playing with hypotheses) and then open them in FigTree for visualization.
Echoing what others have said, I build the custom topology in Mesquite, then export and make it look nice in Figtree.