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Phandango is a fully interactive tool to allow visualisation of a phylogenetic tree, associated metadata and genomic information such as recombination blocks, pan-genome contents or GWAS results. It's an interactive web app, so you just open phandango.net and drag your data files onto the browser, or load any of the provided examples.

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1. How To Use

   1. Panel Layout
   2. Phylogeny
   3. Metadata
   4. Genome Annotation
   5. Recombination Blocks / Pan genome blocks
   6. Line graph
   7. GWAS (Manhatten plots)

2. Input Data Formats

   1. Phylogenies (trees)
   2. Metadata
   3. Genome Annotations
   4. Genomic data
      1. Gubbins (recombination data)
      2. BRAT NextGen (recombination data)
      3. ROARY (pan genome data)
   5. GWAS data

3. Frequently Asked Questions / Problems

   1. Saving as a vector image
   2. Browser quirks
   3. My data didn't display!?!
   4. Is my data being uploaded to a server?
   5. I've found a bug!
   6. Licence

4. Changelog & Roadmap

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Phandango was designed and built by James Hadfield and Simon Harris at the Wellcome Trust Sanger Institute, Cambridge, U.K. James now works on nextstrain at the Fred Hutch in Seattle.

Many thanks to The Centre for Genomic Pathogen Surveillance (CGPS) especially Richard Goater for help and advice.

Phandango makes use of:

• Phylocanvas
• React
• Redux
• canvas2svg