def get_trees(tree_type, tree_size, tree_path):
if tree_type == "binary":
tree = utils.balanced_binary(tree_size)
elif tree_type == "catepillar":
tree = utils.lopsided_tree(tree_size)
elif tree_type == "birthdeath":
tree = utils.unrooted_birth_death_tree(tree_size)
elif tree_type == "kingman":
tree = utils.unrooted_pure_kingman_tree(tree_size)
elif tree_type == "path":
tree = dendropy.Tree.get(path=args.path, schema="nexus")
return tree
import sys, os
sys.path.append(os.path.join(os.path.dirname(sys.path[0]), 'spectraltree'))
sys.path.append(os.path.join(sys.path[0], 'spectraltree'))
import utils
import generation
import reconstruct_tree
N = 1000
num_taxa = 256
jc = generation.Jukes_Cantor()
mutation_rate = [jc.p2t(0.95)]
# Construct data of type 'tree' from class dendropy
namespace = utils.default_namespace(num_taxa)
tree = utils.unrooted_birth_death_tree(num_taxa, birth_rate=1)
for x in tree.preorder_edge_iter():
x.length = 1
#tree = utils.lopsided_tree(num_taxa=num_taxa, namespace=namespace)
#tree = utils.balanced_binary(num_taxa, namespace=namespace)
tree.is_rooted = True
for i in tree.bipartition_edge_map:
if tree.bipartition_edge_map[i] == tree.seed_node.child_edges()[0]:
taxa_half1 = set(i.leafset_taxa(tree.taxon_namespace))
if tree.bipartition_edge_map[i] == tree.seed_node.child_edges()[1]:
taxa_half2 = set(i.leafset_taxa(tree.taxon_namespace))
tree.is_rooted = False
#taxa_half1 = set([taxon for taxon in tree.taxon_namespace if int(taxon.label)<num_taxa/2])
#taxa_half2 = set([taxon for taxon in tree.taxon_namespace if int(taxon.label)>=num_taxa/2])