App for graphing a phylogenetic tree?
March 23, 2016 12:25 AM   Subscribe

What's the best app for graphing out a phylogenetic tree, including pictures, for a fantasy taxonomy? (OSX or iOS, please.)

I think the Omni- family of apps might be in this category, but perhaps there are better/simpler tools out there by now? It's a one-time necessity, so free options preferred - thanks!
posted by progosk to Science & Nature (7 answers total) 2 users marked this as a favorite
Joe Felsenstein at UW Genome Sciences keeps a list of tree plotting/drawing applications which I think are almost all free and open source, if not most.
posted by a lungful of dragon at 12:57 AM on March 23, 2016 [1 favorite]

Best answer: You can also use auto-layout in OmniGraffle for quick cleanup, and then turn off auto-layout to tweak nodes to taste. They have 14-day demo versions of their apps.
posted by a lungful of dragon at 1:04 AM on March 23, 2016

I like FigTree on OSX. Do you have the actual tree in something like newick format?
posted by casaubon at 6:50 AM on March 23, 2016 [1 favorite]

Response by poster: The actual tree is currently just scribbles (fastidious, and illustrated) on paper.

Is there an intelligent workflow beyond just sticking branches and labels and pictures into/onto a document/sheet, so as to print it out into a nice chart poster?

(Within reasonable limits, I'm trying to science-support my teen son's passion for "rigorously" classifying the creatures of a forthcoming computer game.)
posted by progosk at 8:29 AM on March 23, 2016

Best answer: Well, depending on how many creatures there are, expressing the tree in newick format shouldn't be too hard (here's an example). Many programs will read that format. I think FigTree is pretty easy to use on OSX. You could also do it in R.

Putting images on the tip labels is trickier, but this R package and this python package both purport to do it. I was curious so tried out a simple example which you could use as a base.

I'd say there's definitely some nice programming/science educational value here!

Oh and here's another idea -- take a step backwards. What's the classification based on? Of course these days it's all genomes and molecular sequence data, but before that it was morphology [think Darwin's finches]. Write out all the different attributes for all the different creatures, then plug that into an actual phylogeny package to construct a data-driven tree.
posted by casaubon at 10:27 AM on March 23, 2016 [1 favorite]

Response by poster: His phylogeny is definitely morphology-based - but neither of us have anything near the programming chops required to make use of the excellent advice you're offering!

Maybe a graphing app will have to do for now - but I'll see how deeply I can get him to approach this, at least in terms of laying out his thinking.
posted by progosk at 11:07 AM on March 23, 2016

Best answer: I have used Gephi for this in the past.

(Or post your data to a gist and let the crowd tackle it :)

Another term of art: cladogram.
posted by gregglind at 6:22 AM on March 25, 2016

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