The solution for organizing and analysing your microbes.

Pathway Analysis

The pathways page allows coloring biochemical pathways maps according to covered annotations. It is possible to…


The pathways page can be accessed by a right click on the selection of multiple genomes the genome table or from the drop-down menu ‘Tools’ on the top right of the genome table page.

Select a pathway map by entering a search query, for example citrate cycle, and selecting a map of interest. On the demo server, all KEGG-maps are available. Next, select one or more genomes and click on Submit.

It is also possible to select multiple groups of genomes, and to see how they differ.

Click on a shape to learn which genomes cover the contained annotations.

Click on a covered annotation, then on Compare the genes of this annotation to see sequence alignments or compare the gene loci .

pathways demo

Meaning of the colors

If multiple groups are being compared, the shapes are split in as many parts as there are groups. The leftmost color corresponds to first group, etc.

Advanced usage

The color schema can be changed in the settings sidebar (click on settings wheel in the top right corner).

The data behind the plots can be downloaded via the settings sidebar.

The resulting colored pathway map can be downloaded by clicking on the settings wheel, and then on Save as PNG or Save as SVG.