Microreact

Microreact is a tool for visualising genomic epidemiology and phylogeography. Individual nodes on a displayed tree are linked to nodes on a geographical map and/or timeline, making any spatial and temporal relationships between isolates apparent.

The Microreact plugin generates Neighbour-joining trees from concatenated sequences for any selection of loci or schemes and uploads these, together with country and year field values to the Microreact website for display.

Note

While Microreact itself is able to display isolates using GPS coordinates, the BIGSdb plugin is currently limited to the level of country.

Microreact can be accessed by selecting the ‘Analysis’ section on the main contents page.

Jump to the ‘Third party’ category, follow the link to BLAST, then click ‘Launch Microreact’.

Alternatively, it can be accessed following a query by clicking the ‘Microreact’ button at the bottom of the results table. Isolates returned from the query will be automatically selected within the Microreact plugin interface.

Select the isolates to include. The tree can be generated from allelic profiles of any selection of loci, or more conveniently, you can select a scheme in the scheme selector, or from a list of recommended schemes if these have been set, to include all loci belonging to that scheme.

Additional fields can be selected to be included as metadata for use in colouring nodes - select any fields you wish to include. Multiple selections can be made by holding down shift or ctrl while selecting. Click ‘Submit’ to start the analysis.

The job will be sent to the job queue. When it has finished, click the button marked ‘Launch Microreact’.

The generated tree will be uploaded to the Microreact website and displayed. Clicking any node will show its position(s) within the tree, map and timeline. A node on the map may correspond to multiple nodes in the tree or timeline.