Natural Language Processing
Molecular Sequence Analysis
Apache Spark (Databricks)
Cluster Computing (MPI/SNOW)
GPU-Based Processing (CUDA)
High Performance Computing
Genomics, Phylogenetics, Infectious Diseases
Shiny web application for visualizing disease transmittion networks from phylogenetic trees.
Strainhub is designed as a web-based software to generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and a metadata associated file. The software maps the metadata onto the tree and performs a parsimony ancestry reconstruction step to create links between the associated metadata and enable the construction of the network.