Python HKY Examples

Example #1

File: test_nj.py Project: aizeny/stdr

    def test_hky_similarity(self):
        observationsHKY, metaHKY = spectraltree.simulate_sequences(
            seq_len=2_000,
            tree_model=self.reference_tree, 
            seq_model=spectraltree.HKY(kappa=1.5), 
            mutation_rate=0.1,
            rng=default_rng(543),
            alphabet="DNA")

        nj_hky = spectraltree.NeighborJoining(spectraltree.HKY_similarity_matrix(metaHKY))
        self.assertTrue(spectraltree.topos_equal(self.reference_tree, nj_hky(observationsHKY, metaHKY)))

Example #2

    def setUp(self):
        # self.reference_tree = spectraltree.unrooted_birth_death_tree(self.num_taxa, birth_rate=1)
        # self.reference_tree = spectraltree.lopsided_tree(self.num_taxa)
        self.reference_tree = spectraltree.balanced_binary(128)
        # self.reference_tree = spectraltree.unrooted_pure_kingman_tree(self.num_taxa)

        self.observations_hky, self.meta_hky = spectraltree.simulate_sequences(
            seq_len=300,
            tree_model=self.reference_tree,
            seq_model=spectraltree.HKY(kappa=2),
            mutation_rate=0.05,
            rng=np.random.default_rng(234),
            alphabet='DNA')

Example #3

File: test_forrest.py Project: NoahAmsel/spectral-tree-inference

    def test_hky(self):
        observationsHKY, metaHKY = spectraltree.simulate_sequences(
            seq_len=500,
            tree_model=self.reference_tree,
            seq_model=spectraltree.HKY(kappa=2),
            mutation_rate=0.1,
            rng=default_rng(234),
            alphabet="DNA")

        forrest = spectraltree.Forrest()
        self.assertTrue(
            spectraltree.topos_equal(self.reference_tree,
                                     forrest(observationsHKY, metaHKY)))

Example #4

File: SNJ_with metric_correction.py Project: NoahAmsel/spectral-tree-inference

from time import time as _t

import numpy as np

import spectraltree
import metricNearness

N = 100
num_taxa = 60

#################################
## Tree generation
#################################
print("Creating tree")
jc = spectraltree.Jukes_Cantor()
hky = spectraltree.HKY(kappa=2)
mutation_rate = [jc.p2t(0.95)]
# mutation_rate = [0.1]

#reference_tree = spectraltree.unrooted_birth_death_tree(num_taxa, birth_rate=0.5)
reference_tree = spectraltree.lopsided_tree(num_taxa)
# reference_tree = spectraltree.balanced_binary(num_taxa)
# for x in reference_tree.preorder_edge_iter():
#     x.length = 0.5
print("Genration observations by JC and HKY")

observationsJC, metaJC = spectraltree.simulate_sequences(
    N,
    tree_model=reference_tree,
    seq_model=jc,
    mutation_rate=mutation_rate,