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from ete3 import Tree
# Loads a tree with branch lenght information. Note that if no
# distance info is provided in the newick, it will be initialized with
# the default dist value = 1.0
nw = """(((A:0.1, B:0.01):0.001, C:0.0001):1.0,
(((((D:0.00001,I:0):0,F:0):0,G:0):0,H:0):0,
E:0.000001):0.0000001):2.0;"""
t = Tree(nw)
print(t)
# /-A
# /--------|
# /--------| \-B
# | |
# | \-C
# |
# | /-D
# | /--------|
#---------| /--------| \-I
# | | |
# | /--------| \-F
# | | |
# | /--------| \-G
# | | |
# \--------| \-H
# |
# \-E
#
# Locate some nodes
A = t&"A"
C = t&"C"
# Calculate distance from current node
print("The distance between A and C is", A.get_distance("C"))
# Calculate distance between two descendants of current node
print("The distance between A and C is", t.get_distance("A","C"))
# Calculate the toplogical distance (number of nodes in between)
print("The number of nodes between A and D is ", \
t.get_distance("A","D", topology_only=True))
# Calculate the farthest node from E within the whole structure
farthest, dist = (t&"E").get_farthest_node()
print("The farthest node from E is", farthest.name, "with dist=", dist)
# Calculate the farthest node from E within the whole structure,
# regarding the number of nodes in between as distance value
# Note that the result is differnt.
farthest, dist = (t&"E").get_farthest_node(topology_only=True)
print("The farthest (topologically) node from E is", \
farthest.name, "with", dist, "nodes in between")
# Calculate farthest node from an internal node
farthest, dist = t.get_farthest_node()
print("The farthest node from root is", farthest.name, "with dist=", dist)
#
# The program results in the following information:
#
# The distance between A and C is 0.1011
# The distance between A and C is 0.1011
# The number of nodes between A and D is 8.0
# The farthest node from E is A with dist= 1.1010011
# The farthest (topologically) node from E is I with 5.0 nodes in between
# The farthest node from root is A with dist= 1.101
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