Repository for Phytophthora ID, a Microbe-ID cutomized web app for Phytophthora species. Phytophthora-ID is a web site designed for the identification of multiple Phytophthora species using common sequence barcodes (ITS and cox spacer) using BLAST searches against curated databases. Phytophthora-ID has an additional module built in R-Shiny to identify clonal lineages of P. infestans and P. ramorum using SSR markers.
We recommend the users/forkers to read the extensive documentation of the Microbe-ID Github page to understand the construction and deployement of a custom Microbe-ID site.
This repository contains the Bootstrap Twitter html pages of the Phytophthora ID webpage.
Phytopthora-ID contains two main applications: Sequence-ID and Genotype-ID.
Sequence-ID allows identification of species by blasting a query sequence against a custom reference sequence database using BLAST. Sequence-ID has databases for the Internal Transcribed Spaces (ITS) region and the cox spacer.
Genotype-ID allows placement of an unknown genotype in either a minimum spanning network or dendrogram with bootstrap support comparing the queue against an user-created reference database using R and a suite of R packages designed for molecular markers. This version of Genotype-ID includes a modification of the SSR-ID module optimized for clonal lineages of two Phytophthora species, currently, P. ramorum and P.infestans