DeCIFR Microbes

Example NEXUS file download
Example metadata basic download
Example metadata download
Example reference download

To view the network with SplitsTree download here

RGB color selection using ColorBrewer

You can visualize graphs using SpitsTree and the splitstree_colored.nxs and corresponding legend.svg files in the run directory.

reset

Drop Nexus file

Adding columns named bg, fg, edges (color triplet), diameter (pixels), font (PLAIN, ITALIC), shape (circle, square), font-size (0 will hide label), colorize-labels(off/on) will update the nexus file for coloring in Splitstree.
If you just have a metadata file with sample data you can submit the first time with ‘Use added columns’ unchecked and there will be a metadata_updated.csv in the results that can be edited and used a second time with the ‘Use added columns’ checked.

Use added columns (unchecked will automatially assign colors).

Run phangorn (May take longer to finish).

Phipack can require a lot of memory. For a large dataset this can cause the job to reset and fail silently. If a job is running longer than expected then uncheck and resubmit.

Run Phipack

reset

Drop metadata file

Metadata column to create legend for Splitstree: Comma separated list of classes of selected attribute to exclude:

List of strains to exclude, no commas single line or multiline

Annotation:

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SplitsTree

If you use this tool please cite: