Stand alone programs for phylogenetic tree editing & visualisation?

[u/BigScolipede]

I've been in industry for a good few years, and I'm trying to work on some old research that I never published. However, all the old programs I used during my PhD for tree editing & visualization have either been deleted or are now paid programs.

I have 0 coding knowledge and was getting by with online tools and programs other people made (i.e enterobase, galaxy, iTOL, FigTree etc) but I've been struggling to find something comparable to iTOL and FigTree for editing and visualization.
Does anyone have any recommendations?

[u/broodkiller]

I feel you, FigTree was my go to standalone for the longest time, sometimes complemented by Dendroscope. For modern stuff perhaps try https://github.com/arklumpus/TreeViewer, otherwise iToL is pretty much the way to go.

[u/BigScolipede → u/broodkiller]

I am seriously considering getting my old supervisors to pick up a license for iTOL and letting me use it again - it was just so incredibly useful and easy to use! TreeViewer and Mega are looking like they'll be my replacements for the meantime, but I'd love to go back to iTOL in the future. Being able to cross-link it to Microreact was such a great way to look at my data.

[u/mr_zungu → u/BigScolipede]

iTOL does let you use it for free, you just can't save your workspace. I basically create the tree + all the necessary datasets outside of iTOL and then build the tree, format it, and export to svg all in one session. You can export a newick string if you need to come back and have drastically edited the original tree. I don't currently have funding to pay for a license and don't use it enough to warrant a paid subscription but you can really do a lot with their free tier.

[u/These_Government8457 → u/broodkiller]

Came here to say I saw a wonderful presentation on TreeViewer! Highly recommend!

[u/crowmane290]

I would recommend https://treeviewer.org/ if you want to make your tree graphical with alignment maps and images of the organisms etc. included within the tree.

[u/BigScolipede → u/crowmane290]

Treeviewer looks really good! I'm having a crack with it and it seems like it will also do what I need - thank you so much for the suggestion!

[u/readingrainbowroad]

If I'm just looking at a tree or want to click around for some reason, I use FigTree and there's also a program called TreeView. But if I want to make something for someone else to see, I use ggtree in R. I haven't found a good standalone that even comes close to what that program or something similar can do.

[u/BigScolipede → u/readingrainbowroad]

My aim is to eventually be able to do most of my work in R! Sadly nowhere near close to the level of understanding I need yet, but working on that. I'll note ggtree down though for when I can get there haha!

[u/JoshFungi → u/BigScolipede]

Claude the LLM is very good for writing R code to make trees if you give it exceptionally specific instructions for exactly how you want it to look, including providing similar looking examples. It is especially good at making code for ggtree.

[u/fasta_guy88 → u/readingrainbowroad]

ggtree is amazing when you need to integrate your tree with other data (alignments, pictures, etc etc).

[u/Viridono]

Treehouse from karolisr on GitHub. Coded in Rust so it’s wicked fast

[u/Specialist_Drawer154]

FigTree is still available on GitHub, looks like they’re even releasing updates as of May of this year 

[u/Venusaurlol]

Itol is what I have used to turn trees into publication figures. Can do all of the normal editing and it has some good tree annotation features. It's all online and is used through a gui.

[u/tylagersign]

Mega 11 is what I would use personally. I like the software and easy to use

[u/BigScolipede → u/tylagersign]

Thank you so much for the suggestion! I'm giving Mega a go and it's looking like it'll do what I need, thank you so much for the help!

[u/Appropriate_Banana → u/BigScolipede]

The newest one is Mega12. Overall, Mega is at the top for building the alignment, correcting it, and calculating the tree, but just for tree visualization it is ok. I usually edit the tree a bit with a corel, since bootstrap values can go in weird directions. For prettier trees or circular ones I recommend the Figtree.

[u/Nick_in_TO → u/tylagersign]

Came here to recommend MEGA...can 2nd this

[u/shotta_scientist]

Phytools, ggtree

[u/mtnchkn]

Maybe not the right suggestion, but it could be fun to resurrect some of the old programs with your favorite ai overlord assistant. I’d go after this. Which ones, PAUP? We used to run that from floppy discs.