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Preview: Comments on iPhylo: Viewing very large trees

Comments on iPhylo: Viewing very large trees





Updated: 2014-04-24T08:06:22.899+01:00

 



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2008-12-24T08:49:00.000+00:00

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Cyndy, I'd seen TaxonTree before. As you say, it w...

2007-08-30T18:41:00.000+01:00

Cyndy, I'd seen TaxonTree before. As you say, it works better with classifications (as do most large tree viewers that originate in the computer science literature). I'm also not sure what you mean by " browsing of a large tree on the web". It's a Java program that the user has to download and run separately (albeit via Web start). I guess I'm currently hoping we can avoid going down this route.



Don't know if you've seen TaxonTree, our contribut...

2007-08-30T18:21:00.000+01:00

Don't know if you've seen TaxonTree, our contribution to the large tree visualization problem. You can see one of our implementations at our Lep ATOL site, LepTree.net.

It does provide integrated searching and browsing of a large tree on the web. We haven't worked on it recently but have plans for improvements this fall.

Obviously we disagree with TreeJuxtaposer's philosophy about labels, and the current layout works much better with classifications than with phylogenies.

But there it is anyway.



Doh! Simon, did you mean to ask whether Daniel Hus...

2007-08-03T18:27:00.000+01:00

Doh! Simon, did you mean to ask whether Daniel Huson is the mysterious individual in the picture? Not sure, but it looks like him.



No, Inxight is a Xerox spin-off. Daniel has his ow...

2007-08-03T15:58:00.000+01:00

No, Inxight is a Xerox spin-off. Daniel has his own tree viewing software called Dendroscope. It is a Java program and supports viewing large trees. It also includes a rather nice "fish-eye" magnifier to display more detail on selected parts (very like the Dock magnification feature in mac Os X, one of the few widely used fish-eye effects.



Hmm.. is that Daniel Huson?

2007-08-03T14:32:00.000+01:00

Hmm.. is that Daniel Huson?



Hyperbolic trees are fun, and I've used them befor...

2007-08-03T14:09:00.000+01:00

Hyperbolic trees are fun, and I've used them before, as have a few others in this field -- see Tim Hughes' pages on the Walrus 3D hyperbolic browser.

However, they can be distracting to navigate around, and in my experience they work best for trees with high degree (that is, each node has lots of descendants). Hence, they work well for trees such as the hierarchy of files and folders on a computer, or taxonomic classification, but are not great for binary trees (which is what most phylogenies aspire to be).

Lastly, for at least one 2D case the technology is protected by a US Patent held, I believe by Inxight. See US Patent 6901555, for example. Hence, one needs to be very careful using this approach in the US.



Rod,I don't know much things about philoegny but w...

2007-08-03T13:53:00.000+01:00

Rod,
I don't know much things about philoegny but wouldn't be useful to use a hyperbolic tree ? just like http://198.202.68.14/tools/HyperTree.html

also may be of interest : my bookmarks about graphs on connotea

Pierre



Yes, this is the challenge -- small screen, lots o...

2007-08-03T10:38:00.000+01:00

Yes, this is the challenge -- small screen, lots of nodes, limited ability to absorb all the information.

Flash clearly has a lot of potential, but I'm not sure how much of the problem is one of animation. However, it would be fun to see whether at least some of TreeJuxtaposer's functionality could be emulated in Flash.



It seems to me that two closely-related limits nee...

2007-08-03T01:39:00.000+01:00

It seems to me that two closely-related limits need to be kept in mind: screen resolution and human perception. Most screens are going to be physically incapable of showing 1000s of nodes, and, even if they were, how many people could take in that amount of information, anyway? Whatever the solution is, it's not going to be so much about displaying all the information at once as allowing clever ways to focus on areas of the trees.

Flash is not capable of taking advantage of graphics cards, but the new virtual machine in Flash Player 9 is pretty fast--fast enough to do halfway decent 3D animation. Perhaps a good solution would involve Papervision3D, an open-source 3D library for Flash. (Check out the "Rhythm of lines" entry on that blog for a beautiful example of what can be done with it.)



My own suspicion is that Flash/Flex, etc. may be o...

2007-08-03T00:34:00.000+01:00

My own suspicion is that Flash/Flex, etc. may be over-engineering things. To view and interact with really big trees effectively is possibly beyond what these tools can offer. If you read the papers related to TreeJuxtaposer (and it's descendants), there are some sophisticated algorithms involved, some of which depend on making full use of the capabilities of recent graphics cards. This is possibly beyond the capabilities of browser plugins, but not stand alone programs.

Of course, I'd really love a Flash (or whatever) tool to display and interact with trees, but for now I'm looking for a simple technique that scales well (i.e., speedily displays trees with 1000's of nodes).



Whatever the exact implementation, Flash (or Flex)...

2007-08-03T00:26:00.000+01:00

Whatever the exact implementation, Flash (or Flex) seems like the best technology to use for something like this. It does vector and bitmap, it has many tools for interactivity, and the browser plug-in is the most widely-spread one in existence.

I'm doing a project in Flex which requires drawing trees. So far the data in my test files has all fit fairly well, but soon I am going to run into this same problem and will need to come up with a creative solution....



David, I hadn't seen Geni, but had seen iTOL. I'm ...

2007-08-03T00:21:00.000+01:00

David, I hadn't seen Geni, but had seen iTOL. I'm not convinced that a "pan and zoom" approach is the best way forward. It's easy to get lost, and there are issues of how well it scales. For example, I loaded a big bird tree into iTOL and it took a long time to render, and the leaf labels were invisible. I want quick rendering (suitable for viewing lots of trees in a database), and I think the rule has to be "don't draw labels unless they are legible". This is one lesson I draw from TreeJuxtaposer, which displays only a subset of the leaf labels at any one time, but you can always read them.



Rod: I assume you are also aware of iTOL: http://i...

2007-08-02T22:16:00.000+01:00

Rod: I assume you are also aware of iTOL: http://itol.embl.de/index.shtml where you can upload a Newick tree & immediately view it in Flash. Now, if they could offer a download of the resultant Flash file for embedding on a web page, this would be cool way to do it.



This may be out in left field, but have a peek at ...

2007-08-02T21:54:00.000+01:00

This may be out in left field, but have a peek at the kind of thing geneologists have been doing with Flash & AJAX: http://www.geni.com