phyloDB
This project provides a framework for large scale phylogenetic analysis in the form of a Web API, a graph oriented database (Neo4j), and a plugin for the latter. The goal of this project is to allow the representation of large phylogenetic networks and trees, as well as ancillary data, support queries on such data, and the deployment of algorithms for inferring/detecting patterns and for computing visualizations. It was developed in the scope of a master thesis for IST (Instituto Superior Técnico) along with the respective dissertation, article and presentation. This project was accomplished bearing in mind an agile approach using GitHub's project functionality. The unit tests and benchmarks developed are available in the test folder of the code.
The wiki of this project provides documentation of several topics, namely archictecural views, deployment, authentication and the api definition (usage). There are videos supporting the documentation namely, a deployment, an usage example, and a demo.
This solution is hosted and available at http://192.92.147.36:8080 and can be used through HTTP requests, as shown in the wiki. Currently, it only contains the Bartonella bacilliformis taxonomic unit, along with its loci and alleles. It also contains the typing schema used to compose the respective dataset, along with the dataset itself and its respective profiles and isolates.