Is There A Software With Gui That I Can Use To Draw A Phylogenetic Tree Based On The Topology I Want?
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10.9 years ago
Cacau ▴ 520

I want to draw a species tree based on the tree topology that is available already. Is there a software with GUI application that I can use to draw a phylogenetic tree based on the topology I want?

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MS paint. Sorry, I couldn't resist.

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10.9 years ago
David W 4.9k

The venerable old TreeView let's you drag and drop branches. As, I gather, does TreeEdit.

I think you'd need a starting tree with the right number of tips for those programs, alternatively you could do the whole thing within Mesquite.

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Thanks so much!

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10.9 years ago

If you want to capture information from an image (i.e., optical tree recognition), there are a couple of applications for that. One is TreeThief and another is TreeSnatcher. You can find links on Joe Felsenstein's web sitem, which lists all sorts of software, include a sublist of phylogeny plotting software:

http://evolution.genetics.washington.edu/phylip/software.html#Plotting.

But I would not recommend optical tree recognition. If you are going to draw the tree from scratch, then I would suggest to create an input tree in Newick (Phylip) format like this:

( species1, species2, species3, species4 );

with all of your species names, in a plain text file. This will save you the trouble of adding the names later. This will create a tree with every species proceeding from the root node (a "star tree").

Archaeopteryx, FigTree, Mesquite, and PhyloWidget are some viewers that support editing of trees (see A: What is a good phylogenetic tree display program for large data sets?). In Mesquite, you can just choose "open" and then (in the translator dialog box) choose "Phylip (trees)" for the format, and a tree like the one above will be loaded. Then you can use the GUI branch-moving tool (the arrow) to click and drag the branches where you want them.

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Thanks so mucu! I have tried some of them and found Mesquite very useful. The only disadvantage is that newick format is not read by Mesquite.

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Mesquite reads Newick-- it just doesn't call it "Newick". Choose "open" from the file menu and select your file. Mesquite will respond with a translator dialog box asking you to specify the format of the input file. Choose "Phylip (trees)". I edited the answer above to reflect this.

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8.7 years ago
julien.roux ▴ 110

I had a very similar question and didn't find any tool to do this smoothly...

This tool allows to quickly sketch tree and get the output in newick format: http://www.trex.uqam.ca/newick_builder3/index.html

I also used TreeGraph2, which allows tree editing: http://treegraph.bioinfweb.info

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10.9 years ago

if with a "tree topology that is available already" you mean that you have all the tree nodes and branches described, you could use programs like Archaeopteryx (the successor of ATV) that would allow you entering that topology in a wide variety of possibilities, from the newest phyloXML to the more established New Hampshire format.

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