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from ete3 import PhyloTree, TreeStyle
alg = """
>Dme_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEAL--YYASQTDDIKDRREEAH
>Dme_002
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>Cfa_001
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
"""
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()
if __name__ == "__main__":
# Visualize the reconciled tree
t, ts = get_example_tree()
t.show(tree_style=ts)
#recon_tree.render("phylotree.png", w=750)
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