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We have a paper in Nature today! www.nature.com/articles/s41... Several years in the making, Delphy (www.delphy.bio) is one of the tools for outbreak response that we've been building over the last several years with Pardis Sabeti over at the Broad Institute.

Ben Fry

@benfry.com

The project is the brainchild of the inestimable Patrick Varilly, and the tool is 100-1000x faster(!!) than others. For our part, we worked with Patrick on how to make Delphy usable & accessible beyond the handful of PhDs who know the necessary command line incantations to run this kind of analysis.

17/9/26, 10:04 am0 reposts1 like

Ben Fry

@benfry.com

17 Sept

While it's always nice to run faster, what's *actually* exciting about that is the way that it can change the way you work. It means trying things early instead of waiting for perfection. You can immediately identify overall trends, bad data, outliers, etc and fix these problems before the next run.

Ben Fry

@benfry.com

17 Sept

Instead of spending all your time cleaning data first, there's essentially no cost to taking a quick look and proceeding with your research. That's really powerful, because *all data is bad* and the pursuit of what passes for “good” is both time consuming and has its own kinds of badness.

Ben Fry

@benfry.com

17 Sept

(That last part is a post for another time. This is already too long.)

Ben Fry

@benfry.com

17 Sept

Another thing we enjoyed about this project is the ability to visualize the uncertainty, ranges, and error behind its calculations. The output of this analysis is a phylogenetic tree, but like all such trees, it's inherently a lie. It's the least worst lie we can come up with, but it's still a lie.