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The core PhyloD tools were originally created by Jonathan Carlson and David Heckerman of Microsoft Research. We have also included here some invaluable tools that were created by Jennifer Listgarten. Special thanks to Charlie DeZiel for development help, as well as the many collaborators and interns who have worked on these projects. See the publications linked to each tool for full attribution!
Different citations apply to each tool. The appropriate citation will depend on the tool, the sequences used (if you used public sequences the tool provided), the model the tool was trained on, and whether you aligned your sequences using the HMMer tool. We will keep track of all this information and tell you what to cite on your results page. In addition, each tool lists the primary citation where you can find more information about that tool.
A partial list of papers that have used these tools, as well as review articles describing HIV adaptation, is available at Jonathan's webpage.