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