{
"name": "",
"children":[
{
 "label": "JASPAR_Coordinator_n181"
}
]
}
{
"name": "",
"children":[
{
 "label": "JASPAR_CTCF_DOWN_1_n175"
}
]
}
{
"name": "",
"children":[
{
 "label": "JASPAR_CTCF_DOWN_2_n176"
}
]
}
{
"name": "",
"children":[
{
 "label": "JASPAR_CTCF_DOWN_n177"
}
]
}

A text-delimited file where each line contain the next fields. 1: Motif file path; 2: Motif collection name; 3: Motif format (Mandatory). It does not expect a header, but it expects those columns in the indicated order.

Comparison metric used to build the hierarchical tree. [Default: "%default" . Options: cor, Ncor]

Linkage/agglomeration method to build the hierarchical tree. [Default: "%default" . Options: average, complete, single]

number of cores to run in parallel. [Default "%default"]

Export hierarchical tree in Newick format. [Default "%default"]

Export heatmap with clusters in PDF. [Default "%default"]

Radial representation of all motifs aligned. In this alignment the thresholds are ignored, however the clusters are detected and highlighted in the radial tree [Default "%default"]

Cell colors in clusters heatmap. [Default: "%default"]. Options: any colorBrewer palette, see colorbrewer2.org for details

Number of classes to create color palette in clusters heatmap. [Default: "%default"]. Options: depends on the selected colorBrewer palette, see colorbrewer2.org for details

Pearson correlation threshold. [Default "%default"]

Normalized Pearson correlation threshold. [Default "%default"]

Minimum number of aligned positions between a pair of motifs. [Default "%default"]

When TRUE only returns the alignment, clusters and motif description tables. Comparison results, plots and trees are not exported. [Default "%default"]

Motif annotation table, when this file is provided with the '--radial_tree = TRUE' option add annotations to the radial tree. A tab-delimited file with at least the following columns : 1) motif_id, 2) class ID, 3) collection. If the input motifs are separated in many collections, concatenate all the annotations in a single file.