phyloTree takes tree in json format as input. Each internal node as a .children array with descendent nodes. Furthermore, each node has a .attr attribute that stores meta data and branch length information.
phyloTree is built around a data structure that stores the data and current state of the tree.
tree = {
nodes: [node1, node2, ...], //linear array of nodes
tips: [tip1, tip2, ...], //terminal nodes, subset of all nodes
internals: [node1, node2, ...], //internal nodes, subset of all nodes
tipAttributes: { } , //object storing styles and attributes of tips
branchAttributes: { } , //object storing styles and attributes of branches
tipElements: { } , //d3 elements corresponding to the tips
branchTbarElements: { } , //d3 elements corresponding to the branches
branchStemElements: { } , //d3 elements corresponding to the branches
}
Upon instantiation, phyloTree generates this data structure and wraps the input tree into a custom node structure where the original node is stored as .n.
Phylotree support different tree layouts including rectangular layout, radial layout, unrooted layout and the possibility to plot a distance attribute against sampling time
PhyloTree can use any numerical parameter as branch length. Such quantities can be stored in attr. In addition phyloTree implements a cladogram view, discrete number of branchings to the root is used as distance.