Which formats are accepted for hierarchies?

There is a variety of accepted formats. The most easy way to create your own hierarchy is to use the treemap simple format (TMS):

Root                
    Cluster 0            
        Cluster 0.0        
            Cluster 0.0.0    
                Cluster 0.0.0.0
                Cluster 0.0.0.1
                Cluster 0.0.0.2
                Cluster 0.0.0.3
            Cluster 0.0.1    
                Cluster 0.0.1.0
                Cluster 0.0.1.1
...

TMS format is easy to read, but you need to be carefull since the order of the rows is important.

Another format is the path format (PATH):

Root    Cluster 0    Cluster 0.0    Cluster 0.0.0    Cluster 0.0.0.0
Root    Cluster 0    Cluster 0.0    Cluster 0.0.0    Cluster 0.0.0.1
Root    Cluster 0    Cluster 0.0    Cluster 0.0.0    Cluster 0.0.0.2
Root    Cluster 0    Cluster 0.0    Cluster 0.0.0    Cluster 0.0.0.3
Root    Cluster 0    Cluster 0.0    Cluster 0.0.1    Cluster 0.0.1.0
Root    Cluster 0    Cluster 0.0    Cluster 0.0.1    Cluster 0.0.1.1
...

PATH is also easy to read. Its advantage is that each row contains the full path to a certain leaf of the hierarchy making the rows independent from each other.

You can download our demo data sets to review these formats and use them as templates.

Besides these two formats Paver also accepts Newick, KEGG Go and OBO files.