Showing posts with label supertrees. Show all posts
Showing posts with label supertrees. Show all posts

Tuesday, July 7, 2009

Large Tree Extraction, Viewing, and Printing

Extracting trees from various idiosyncratically formatted databases is a pain, as is the task of printing very large trees for visual inspection of showing off. Many software packages are competent or good at one or both sets of tasks--I use some combination of APE package for R and FigTree, which work well for most of my needs, but not all. There are two new tools that help partly solve a couple of vaguely related problems.

Archaeopteryx, written by Christian Zmasek, is a Java-based application potentially useful in broad comparative analyses for extraction of trees from various source formats. With open source Java and Ruby libraries, it reads and displays trees in common formats (e.g. newick and nexus) as well as NCBI Taxonomy, TOL, and PhyloXML. For a nice example, take a look at the amphibian tree, then go to 'View as Text' and copy the newick formatted tree. Why? If you were to wish to print this or another large tree, you'd be out a nice chunk of time, and experience moderate hassle. No longer.

Tred, Rick Ree's web-based tree printing tool, can import, manipulate, and print very large trees. The most exciting feature for me is the duplication of sections near the margins for easy pasting of multi-page trees! The amphibian tree can be easily printed over three pages, taped together at convenient overlaps, and posted above your desk.

I can barely contain the urge to outdo the Hillis and Bull Lab tree, pictured above, by using the above tools to print out and unfurl a gigantic tree of life from Sears Tower. (Nevermind the uncertainty or accuracy.) A cheap way into the Guinness Book of World Records?

[Thanks to MudPuppy for pointing out Archaeopteryx!]

Tuesday, February 10, 2009

Phylografter (beta)

Rick Ree just made publicly accessible his new immensely useful program for creating conglomerated trees, Phylografter (beta version). While tree grafting is an old business (and it may soon be superseded by GenBank trawling and mega-phylogeny reconstruction), our DNA taxon sampling is not stellar for most groups, and anyone who has made glomograms by hand will immediately recognize its utility

Phylografter is a web2py-based application that allows users to upload trees or use existing ones in order to join them for the purpose of creating a single large phylogeny. The current demo version can be downloaded or run on a web server, and handles up to 7,000 tips. There are thousands of trees already uploaded into the tree database, which can be used to create new glomograms. It is presently a bit plant-heavy--not a big surprise, given the context of its creation. [Read more at EOL.]