Welcome

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Microbe-ID is a toolbox that can readily be customized for any taxonomic group or species for sequence based identification of species or marker-based identification of strains.

Microbe-ID aims to:

• Outline a method for development of a species and strain identification website using existing open source, online resources.
• Integrate existing population genetic analyses and visualizations into the genotype identification tool in order to improve genotype diagnostic capabilities.

This site provides all code and applications necessary for creating a website for species identification or strain genotyping.

Components

Microbe-ID is comprised by two main applications: Sequence-ID and Genotype-ID.

• Sequence-ID allows identification of species by blasting a query sequence for any locus of interest against a custom reference sequence database using BLAST
• 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

Microbe-ID groups these two applications in a HTML5 framework based on Bootstrap that links both applications into a simple, web-ready site to be deployed locally or in a server.

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Visit the project page in Github for details in requirements, installation and deployment of Microbe-ID at http://github.com/grunwaldlab/Microbe-ID

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