What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
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12.5 years ago
Niek De Klein ★ 2.6k

I'm looking for a phylogenetic tree display program that can handle large data sets well. I'm currently using NJ-plot and phylip but I find that these get unclear with large data sets. I'm using clustalX for the multiple sequence alignment and to draw the trees.

Thanks!

tree tool phylogenetics viewer • 55k views
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Hasn't this been covered already? take a look: Huge Tree Visualization

EDIT: Link updated by @RamRS on 30-Aug-2019.

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provided link doesn't go anywhere... :(

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Maybe you could be a little more specific- what do you mean by "large data sets"?

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12.2 years ago
lh3 33k

This is an old question, but as I have seen it...

In general, a good start is the list of tree editors maintained by Richard Christen. It is quite comprehensive. I will give my personal experiences for the few I have used. In the following, a small tree has <100 leaves, a medium tree 100-1000 leaves, and a large tree has 1000-10000. I have not tried huge trees with >10000 leaves.

• Archaeopteryx. This is my favorite. It is responsive given large trees and is one of the few supporting topology editing. Nonetheless, the circular view, which is in alpha, is not as good as others. I do not like its black background, either.

• FigTree. A nice tree viewer. Work efficiently with medium to large trees. It is more versatile than Archaeopteryx on viewing (e.g. the fish-eye mode and the circular layout). No topology editing.

• Dendroscope. A viewer (almost no editing options) designed for huge trees. The selling point is its efficiency, better than both FigTree and Archaeopteryx. Nonetheless, it does not seem to aim to produce publication-ready figures (e.g. no subtree highlighting). The circular view, like in Archaeopteryx, looks ugly because texts are not rotated.

• Jstree. My hobby. The first Javascript based tree editor, supporting operations such as subtree cut-and-paste. In firefox/opera/chrome/safari, it is pretty responsive for medium to large trees.

• PhyloWidget. It has a very impressive user interface, smooth and responsive given large trees. It supports topology editing. My major complaints are: a) I frequently scroll the tree out of the canvas but do not know how to get it back quickly; b) at least on my laptop, it is eating up CPU without actually doing anything.

• iTOL. A very nice tree viewer (no editing) written in Flash, but the responsiveness is not as good as those Java-based viewers. For medium trees, its rectangle view only displays the first tens of leaves.

• TreeGraph2. As is stated in its paper, treegraph2 mainly aim to produce beautiful high-quality figures for small trees. It supports many operations on trees, but its responsiveness is very bad.

• Mesquite. A very comprehensive software suite. It is efficient enough for large trees, but the user interface is not very friendly.

• TreeDyn. I have heard a lot of good things about it, but unfortunately, its Mac binary is not working in Mac OS X 10.6, so I have not tried.

• TreeViewJ. Nice UI, but not efficient enough for medium trees.

• Treevoletion. Nice UI, but inefficient for medium trees.

My recommendation is: FigTree, Dendroscope or Archaeopteryx for tree viewing; Archaeopteryx for topology editing; TreeGraph 2 (for small trees only) for publication-quality figures; Jstree for a web interface.

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Just a note on Dendroscope : you can highlight the nodes and branches of the tree using the built-in editor (which is painful) or use a script to parse a Dendroscope output file. Example tree highlighter code @ http://pastebin.com/wA508SCD

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I see, but the point of a viewer is not to write scripts... Anyway, thanks.

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I am searching for command line tools that align and visualize tree of upto 200000 genome sequences with everything looking good and clear. I tried with above tools along with plottree ,but the plot is not interactive and looks all overlapped ,nothing can be predicted from that. Is there any tool that generate plots similar to auspice of nextstrain?

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12.5 years ago

I would recommend that you take a look at iTOL. It is purely web based, can visualize trees with several thousand nodes, and additionally allows you to map other data onto your tree for visualization.

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12.5 years ago

For large scale phylogenies I strongly recommend Dendroscope.

Beside dealing extremely well with a large amount of leaves, one of its advantages is the possibility to select leaves via a file containing IDs. Like some other tree visualization softwares, it allows SVG export so that you can work on the graphical aspects of your tree in a SVG editor such as Inkscape.

Another solution would be treedyn, needs some time investment to understand the syntax but it's worth it.

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When I want to quickly see a few leaves in a large tree (thousands of branches), I open search, toggle "regex" on and then search my taxa by (partial) name separated by | and click "show all". Dendroscope then highlights all matches, which is super handy.

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12.5 years ago

I would recommend Phylowidget. A standalone version is available, as is the source code (Java) and it can cope with large trees. The nodes may be edited and it guarantees a minimum text size for large trees.

Alternatively, TreeGraph 2 is another good option. Also open source (Java) and allowing various edits and annotation.

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12.5 years ago
Alex ▴ 150

I would recommend figtree (http://tree.bio.ed.ac.uk/software/figtree/), it is a good program, maybe you will require some tine to figure out how to use it, but it is not that difficult. Also, i don't know how big is your data but you can have nice figures for presentations and papers.

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I would describe Figtree as "good enough". It gets the job done, especially if you have only a few dozen branches. It has some nice editing features, like coloring branches of a subtree, making a rectangle around a subtree you want to emphasize etc.

But the program itself is not the most user friendly. There is no undo. You do something wrong, and you have to start over (unless your wrong operation can be overwriten with different one, lucky you!). Exporting images is even worse - the dimensions depend on the window of your Figtree! You want different dimensions? Resize your window and try exporting again! I did not find any other way to set dimensions for exported pictures.

So most of the users of Figtree I know tell me this: Make the tree look roughly how you want there, then export it as vector image (SVG, PDF, EPS), open it in Inkscape and finish it there.

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12.2 years ago
Botond Sipos ★ 1.7k

The APE R package also comes handy when drawing large trees. It allows the tuning of tree aesthetics by scripting. Check out this gallery.

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12.5 years ago

Hii, if you have too many sequences, and a lot of them cluttering up at a spot, may be you could look at multiple sequence alignment (I have used MEGA for this) and look if they are very identical. If you find lot of them identical, you could probably do clustering(CD-HIT) and then build a tree with the representative sequences from the clusters obtained.

iTOL, Treeview, MEGA, ATV are good tools out there to visualize trees.

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12.2 years ago
Farhat ★ 2.9k

If by large datasets you means trees with a large number of nodes you could try using Walrus http://www.caida.org/tools/visualization/walrus/ The gallery on their website shows trees with several tens of thousands to several hundred thousand nodes.

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10 months ago
Theo ▴ 20

Taxonium is designed for exploring very large phylogenetic trees (many millions of nodes).

PhyloCanvas.GL, implemented in MicroReact also scales to large trees.

Edit: COI disclosure - I am the author of the first tool. I have no connection with the second tool.

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It would be nice if you disclosed the bias since you seem to be promoting your own software.

It will likely be more impactful to create a separate post explaining your program's benefits in detail rather than attaching these short messages to threads that are 10+ years old.

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Hi there, I added the COI - thanks for flagging. Re: why I am adding to this post: when I first wanted to view a tree of millions of nodes in the browser ~ a year ago, I googled and these threads came up at the top, but did not include a tool that permitted this. So I've added two newly developed tools that do for people in a similar position.

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