# Welcome to StrainHub! ## About StrainHub StrainHub is designed as a web-based software to generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata. Today, StrainHub consists of a standalone R package, a code-free web application, and a containerized version for running the web app locally. 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. Users have the option to build a tree utilizing their method of preference outside StrainHub or build a tree utilizing a FASTA file within StrainHub with the Neighbor-Joining algorithm. Alternatively, the user can skip the StrainHub ancestry reconstruction step by generating a maximum clade credibility tree (MCC) through BEAST phylogeography or input a previously generated list of edges in order to build the transmission network. Additionally, the user can input a file with geographic cooordinates associated with the character of interest and have the network plotted into a map. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.strainhub.io/master.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.