This site provides all code and applications necessary for creating a website for species identification or genotyping. A working implementation of Microbe-ID for plant pathogens in the genus Phytophthora can be found at Phytophthora-ID. This site allows identification of species based on ITS or cox-spacer sequences as well as placement of SSR genotypes into known reference populations.
To install Microbe-ID on your server you need the following components and applications:
- Your own linux server
- A website based on bootstrap to host your version of Microbe-ID
- A self-hosted shiny R server session running on your server
- Two shiny R scripts for server and user interface (UI)
- Your custom fasta database for Sequence-ID
- Your custom tab-delimited text file for Genotype-ID compatible with the poppr R package
This site was built solely with open source components.
Designed and built by members of the Grunwald lab. For questions, please contact Javier Tabima.