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from ete3 import PhyloTree
# Creates a gene phylogeny with several duplication events at
# different levels. Note that we are using the default method for
# detecting the species code of leaves (three first lettes in the node
# name are considered the species code).
nw = """
((Dme_001,Dme_002),(((Cfa_001,Mms_001),((((Hsa_001,Hsa_003),Ptr_001)
,Mmu_001),((Hsa_004,Ptr_004),Mmu_004))),(Ptr_002,(Hsa_002,Mmu_002))));
"""
t = PhyloTree(nw)
print("Original tree:\n")
print(t)
#
# /-Dme_001
# /--------|
# | \-Dme_002
# |
# | /-Cfa_001
# | /--------|
# | | \-Mms_001
# | |
#--| | /-Hsa_001
# | | /--------|
# | /--------| /--------| \-Hsa_003
# | | | | |
# | | | /--------| \-Ptr_001
# | | | | |
# | | | | \-Mmu_001
# | | \--------|
# \--------| | /-Hsa_004
# | | /--------|
# | \--------| \-Ptr_004
# | |
# | \-Mmu_004
# |
# | /-Ptr_002
# \--------|
# | /-Hsa_002
# \--------|
# \-Mmu_002
# Create a dictionary with relative ages for the species present in
# the phylogenetic tree. Note that ages are only relative numbers to
# define which species are older, and that different species can
# belong to the same age.
species2age = {
'Hsa': 1, # Homo sapiens (Hominids)
'Ptr': 2, # P. troglodytes (primates)
'Mmu': 2, # Macaca mulata (primates)
'Mms': 3, # Mus musculus (mammals)
'Cfa': 3, # Canis familiaris (mammals)
'Dme': 4 # Drosophila melanogaster (metazoa)
}
# We can translate each number to its correspondig taxonomic number
age2name = {
1:"hominids",
2:"primates",
3:"mammals",
4:"metazoa"
}
event1= t.get_common_ancestor("Hsa_001", "Hsa_004")
event2=t.get_common_ancestor("Hsa_001", "Hsa_002")
print()
print("The duplication event leading to the human sequences Hsa_001 and "+\
"Hsa_004 is dated at: ", age2name[event1.get_age(species2age)])
print("The duplication event leading to the human sequences Hsa_001 and "+\
"Hsa_002 is dated at: ", age2name[event2.get_age(species2age)])
# The duplication event leading to the human sequences Hsa_001 and Hsa_004
# is dated at: primates
#
# The duplication event leading to the human sequences Hsa_001 and Hsa_002
# is dated at: mammals
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