Interactive Tree of Life (iTOL)

The ITOL plugin allows you to generate and visualise phylogenetic trees calculated from either concatenated sequence alignments or from allelic profiles of selected loci (or the loci belonging to a particular scheme). Neighbour-joining trees (generated by ClustalW) and Approximately-Maximum Likelihood trees (generated by FastTree) are supported from concatenated sequences. Neighbour-joining trees using RapidNJ (as implemented in GrapeTree) are supported for profiles. Datasets can include metadata which allows nodes in the resultant tree to be coloured.

The function can be accessed by expanding the ‘Analysis’ section on the main contents page.

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

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Select the isolates to include. The tree can be generated from any selection of loci, or more conveniently, you can select a scheme in the scheme selector, or in the list of recommended schemes if these have been set up, 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 in the ‘iTOL datasets’ list. Multiple selections can be made. You can also choose how nodes are labeled by metadata - either by colouring the labels or using coloured strips.

Click ‘Submit’ to start the analysis.

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The job will be sent to the job queue. When it has finished, the generated tree and associated metadata will be uploaded to the Interactive Tree of Life website (https://itol.embl.de/). Click the button marked ‘Launch iTOL’.

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Your browser will open the iTOL website with your tree.

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You can manipulate the tree in the browser, and display metadata by selecting the appropriate toggle.

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The tree layout can be changed by clicking the ‘Basic tab’ and, for example, selecting a circular display mode.

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See the detailed documentation on the iTOL website for more information about manipulating and exporting trees.