Welcome to the web home of the Stoltzfus research group at The Institute Formerly Known as CARB.

About Us

The Computational and Analytical Molecular Evolution Lab (camel) is the home of the Stoltzfus group at IBBR.  We use our minds and our computers to address issues in evolutionary genetics, molecular evolution, and bioinformatics.  We are especially interested in one particular scientific challenge, which is to understand the role of mutation as an evolutionary cause, and one particular techological (in some respects) challenge, which is to improve the interoperability of software and data resources used by evolutionary researchers

Phylotastic update

Posted Mon, 10/01/2012 - 16:33 by arlin

The Phylotastic project-- launched at a recent NESCent hackathon-- aims to develop software, standards and strategies to provide computable, convenient, and credible access to the Tree of Life.  You can learn more about it at phylotastic.org.  

The Phylotastic project— launched at a NESCent hackathon in June— aims to develop software, standards and strategies to provide computable, convenient, and credible access to the Tree of Life.

Phylotastic - making the Tree of Life useful (really) for scientists

Posted Thu, 03/22/2012 - 08:28 by arlin

An analysis of the re-use of phylogenetic trees in the research literature (Stoltzfus, et al., in progress-- see the story on it) showed some notable patterns.   Trees aren't archived very often, and so they aren't re-used very often.  We expected that.  

But we found something we didn't expect-- a case of re-use so frequent that, in a targeted sample of 40 phylogeny-related studies, we found 5 studies that use the same tree from the same source-- "Phylomatic" (Webb & Donoghue).  Phylomatic provides the APG (Angiosperm Phylogeny Group) "megatree" with ~100K nodes for flowering plants, and provides operations for pruning and grafting.  The result is that users with a list of, e.g., 285 plant species, can go to Phylomatic and get a species tree for their precise set of 285 species. 

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