def yule(n):
"""
Returns a list of tuples containing all the shapes of n leaves that can be obtained under the Yule model and their
corresponding probability.
:param n: `int` instance.
:return: `list` instance.
"""
for t, p in phylo_yule.yule(n):
yield phylotree_to_shape(t), p
def yule_from_t(sh, prob):
"""
Returns a list of tuples containing each shape obtained from `Shape` sh (assuming sh has probability prob) with
their associate probability under the Yule model.
:param sh: `Shape` instance.
:param prob: `function` instance.
:return: `list` instance.
"""
for t, p in phylo_yule.yule_from_t(shape_to_phylotree(sh), prob):
yield phylotree_to_shape(t), p
def cherry_picking(tree, k):
if tree.is_leaf():
return [tree]
elif tree == Shape.CHERRY:
return [Shape.LEAF]
else:
def go(t, i, d): # for binary eyes only
if d != k and not (t.is_leaf() or t.is_cherry()):
chs = [go(ch, i, d + 1) for ch in t.children]
if any(ch is None for ch in chs):
return None
else:
return PhyloTree(None, sorted(chs))
elif d != k and (t == PhyloTree(
None, [PhyloTree(i), PhyloTree(i + 1)]) or t == PhyloTree(
None,
[PhyloTree(i - 1), PhyloTree(i)])):
return None
elif d == k and (t == PhyloTree(
None, [PhyloTree(i), PhyloTree(i + 1)]) or t == PhyloTree(
None,
[PhyloTree(i - 1), PhyloTree(i)])):
return PhyloTree(i)
elif t == PhyloTree(i):
return None
else:
return t
n = count_leaves(tree)
phyl = shape_to_phylotree(tree, gen=int)
ts = []
for i in range(n):
t = go(phyl, i, 1)
if t:
ts.append(phylotree_to_shape(t))
return unique(sorted(ts))
def sim_yule_from_t(t):
return phylotree_to_shape(phylo_yule.sim_yule_from_t(
shape_to_phylotree(t)))
def sim_yule(n):
return phylotree_to_shape(phylo_yule.sim_yule(n))