Here you can find information about any software projects I have developed or that I am contributing too. This is by no means a comprehensive list, and I make no promises about how often I will update it. If you want a likely more current list, visit my account on Github.



Website | Source Code | Citation

Phyloboost is a python pipeline that allows the reconstruction, augmentation and visualizaton of the similarity-cluster-based tree sets constructed from an input dataset of sequences. The end point is a data object that can be explored or used to quantify the phylogenetic signal present in whatever dataset acted as the input. While originally developed as a tool to allow the synthesis and calculation of the phylogenetic signal in Genbank for Eukaryotes, it will work on any large set of DNA or RNA sequence data.



Website | Source Code | Citation

Phylografter is a database / software tool I contribute to as part of my post-doc at the Field Museum. It was originally written and is maintained by Richard Ree. The software and database provide a method for archiving source trees, i.e., trees derived from published studies, stored node-by-node, with associated data (publication info, aligned sequences, Genbank ids, gene and genome info, support values, age estimates, etc.).


Open Tree of Life Project

Website | Source Code | Citation

As part of my post-doc work, I contributed in varying degrees to the Open Tree of Life project. The goal of this project is to produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This includes the development of software tools for scientists to update and revise the tree as new data come in.