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. 2016 Jul 19;4:e2222. doi: 10.7717/peerj.2222

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©2016 Davis II et al.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

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DNA sequence information can be used to reveal the identity of the causative agent (unknown isolate) of disease. Tools associated with “Gall Isolate Typing” and “Phytopath-type” use 16S rDNA or pathogen-specific MLSA gene sequences to infer the identity of the isolate by comparing the sequences to manually curated sequence databases. Tools associated with “Whole Genome Analysis” and “Vir-Search” use Illumina short sequencing reads to characterize pathogenic isolates. The former tab provides downloadable tools to infer genetic relatedness based on SNPs (WGS Pipeline) or average nucleotide identity (Auto ANI). The “Vir-Search” tab provides an on-line tool to quickly map short reads against a database of sequences of virulence genes.