PhyNetPy is a network first library, as there is no separate tree class that is required to be void of reticulations or hybridizations. Every network or tree is represented the same way, as a directed acyclic graph (the DAG class).
To create a network is very easy and straightforward:
from PhyNetPy.Graph import DAG
#Can initialize as an empty graph
tree = DAG()
#To make it a network, simply add in individual nodes
#one at a time, or pass in an array of nodes
tree.addNodes(individualNodeObj)
tree.addNodes(arrayOfNodeObjs)
#same applies to adding edges
tree.addEdges(individualEdge)
tree.addEdges(arrayOfEdges) #Where an edge can just be [NodeObj, NodeObj2]
#Now you have a complete network. To grab the newick representation...
newickStr = tree.newickString()
#You can now visualize your graph with IcyTree
#You can also initialize trees with node and edge lists
tree2 = DAG(edgeList) #add nodes later
tree3 = DAG(nodes = nodeList) #add edges later
tree4 = DAG(edgeList, nodeList) #add both now
#To see a description of all the nodes in your graph:
tree.printGraph()
A Node object has the following initialization parameters, all of which are defaults:
- branchLen = None
- parNode = [ ]
- attr = { }
- isReticulation = False
- name = None
from PhyNetPy.Node import Node
#Can initialize as an empty Node
new_node = Node()
#To set the branch length
new_node.setBranchLength(num)
#To get the branch length
node_len = new_node.branchLen()
#To add a parent (must be a Node or UltrametricNode obj)
new_node.addParent(par_node)
#or to set the parent
new_node.setParent(par_node)
#To set the name of a Node
new_node.setName("Homo Sapiens")
#To get the name of the Node
node_name = new_node.getName()
#To set a custom attribute
new_node.setAttribute(attribute, value) #i.e "t" : 5.4
#To look up an attribute
attr_val = new_node.attrLookup(attribute) #i.e "t" returns 5.4
#To visualize the values contained in a Node obj
new_node.asString()
#A more typical way to create a Node
new_node2 = Node(parNode = [par_node], attr = {"t":5.4}, name = "species2")