Tools

empiricIST: a software that allows for accurate estimation of selection coefficients and credibility intervals from bulk competitions

empiricIST is an integrative framework for the analysis of bulk competition data, and includes separate programs for processing raw sequence data and correcting for sequencing errors, obtaining statistically meaningful estimates of selection coefficients in a fast and efficient manner, and for providing ready-to-use summary statistics of the MCMC analysis and its associated parameter estimates.

empiricIST GitHub repository

Also check out our manuscript on The fitness landscape of the codon space across environments to see an example of how empiricIST can be used. We used the selection coefficients estimates to quantify changes in the topology and the topography of the codon fitness landscape in different environments considering non-synonymous and synonymous mutations.

Interactive online tool to visualize the loss of a neutral Dobzhansky-Muller incompatibility in the presence of gene flow

Go directly to the tool by clicking below:

Interactive DMI web app

Interactive online tool for experimental design of high-throughput bulk competitions

Go directly to the tool by clicking below:

Optimize high-throughput bulk competitions

Or download and read the corresponding manuscript first: A statistical guide to the design of deep mutational scanning experiments – also available as free preprint.

Javascript bookmarklet for toning down styles/appearance of suggestions and comments in shared google docs with (many) suggestions

Check out the accompanying website:

Website for our GDocs Bookmarklet

The Bookmarklet will (temporarily) add three new icons in your Google-Docs menu, which allow to toggle comments by authors, toggle display of newlines and tabs, apply user or google styling for suggestions and comments (watch the video on the website to see it in action).

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