LINtree

LINtree is a tool to infer prefix trees with branch lengths from sets of Life Identification Number® (LIN®) codes. Such LIN-based prefix trees are very useful to reflect the phylogenetic relationships among genomes typed by cgMLST where LIN codes have been assigned. Once the tree has been generated, the resultant Newick file is uploaded to iTOL for visualisation (if enabled) along with selected metadata that can be used to annotate it.

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Only isolates with an assigned LIN code can be included in the tree.

Lintree can be accessed by selecting the “Third party” section on the main contents page.

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Jump to the “Third party” category, follow the link to LINtree, then click “Launch LINtree”.

LINtree can be accessed from the contents page by clicking the “LINtree” link.

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

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Select the isolates to include. If there is more than one scheme in the database that has LIN codes assigned, then select the required 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. LIN codes are selected by default.

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.

Note

LINtree has been developed by Alexis Criscuolo. The code can be found at https://gitlab.pasteur.fr/GIPhy/LINtree.

Genome Informatics & Phylogenetics (GIPhy), Centre de Ressources Biologiques de l’Institut Pasteur (CRBIP), Institut Pasteur, Paris, France

LIN is a trademark registered by This Genomic Life, Inc, Floyd, VA, USA.