def get_example_tree():
# Performs a tree reconciliation analysis
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);"
genetree = PhyloTree(gene_tree_nw)
sptree = PhyloTree(species_tree_nw)
recon_tree, events = genetree.reconcile(sptree)
recon_tree.link_to_alignment(alg)
return recon_tree, TreeStyle()
def get_example_tree():
# Performs a tree reconciliation analysis
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);"
genetree = PhyloTree(gene_tree_nw)
sptree = PhyloTree(species_tree_nw)
recon_tree, events = genetree.reconcile(sptree)
recon_tree.link_to_alignment(alg)
return recon_tree, TreeStyle()
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>Mms_001
MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
>Hsa_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
>Ptr_002
MAEIPDATIQ-FMALTNVSHNIAVQY--EFGDLNEALNSY--YQTDDQKDRREEAH
>Mmu_002
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>Hsa_002
MAEAPDETIQQFM-LTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
>Mmu_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
>Ptr_001
MAEIPDATIQ-FMALTNVSHNIAVQY--EFGDLNEALNSY--YQTDDQKDRREEAH
>Mmu_001
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
"""
# Performs a tree reconciliation analysis
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);"
genetree = PhyloTree(gene_tree_nw)
sptree = PhyloTree(species_tree_nw)
recon_tree, events = genetree.reconcile(sptree)
recon_tree.link_to_alignment(alg)
# Visualize the reconciled tree
recon_tree.render("phylotree.png", w=750)
#---------| | \-Mms_001
# | /--------|
# | | | /-Hsa_001
# | | | /--------|
# | | \--------| \-Ptr_001
# \--------| |
# | \-Mmu_001
# |
# | /-Ptr_002
# \--------|
# | /-Hsa_002
# \--------|
# \-Mmu_002
#
# Let's reconcile our genetree with the species tree
recon_tree, events = genetree.reconcile(sptree)
# a new "reconcilied tree" is returned. As well as the list of
# inferred events.
print "Orthology and Paralogy relationships:"
for ev in events:
if ev.etype == "S":
print 'ORTHOLOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.orthologs)
elif ev.etype == "D":
print 'PARALOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.outparalogs)
# And we can explore the resulting reconciled tree
print recon_tree
# You will notice how the reconcilied tree is the same as the gene
# tree with some added branches. They are inferred gene losses.
#
#
# /-Dme_001
