def random_coal(self, nspecies=None, names=None):
if names and nspecies:
if not nspecies == len(names):
nspecies = len(names)
elif names and not nspecies:
nspecies = len(names)
elif not names:
if not nspecies:
nspecies = 16
names = taxonnames.names[:nspecies]
if nspecies > len(taxonnames.names):
names.extend(['Sp{0}'.format(i) for i in
range(len(taxonnames.names) + 1, nspecies
+ 1)])
taxon_set = dpy.TaxonSet(names)
tree = treesim.pure_kingman(taxon_set)
newick = '[&R] ' + tree.as_newick_string()
if not newick.endswith(';'):
newick += ';'
return Tree(newick)
#! /usr/bin/env python
import dendropy
from dendropy import treesim
taxa = dendropy.TaxonSet(["z1", "z2", "z3", "z4", "z5", "z6", "z7", "z8"])
tree = treesim.pure_kingman(taxon_set=taxa,
pop_size=10000)
print(tree.as_string("newick"))
print(tree.as_ascii_plot())
def runTest(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = RepeatedRandom()
t = treesim.pure_kingman(dendropy.new_taxon_set(100), rng=_RNG)
assert t._debug_tree_is_valid()
def generate_trees_Kingman(Pop_size=49,rang=314):
from dendropy import TaxonSet, TreeList, treesim
taxa = TaxonSet()
trees = TreeList()
trees=[treesim.pure_kingman(taxon_set=taxa, pop_size=Pop_size) for x in range(rang)]
return trees
def runTest(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = RepeatedRandom()
t = treesim.pure_kingman(dendropy.new_taxon_set(100), rng=_RNG)
assert t._debug_tree_is_valid()