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# cogent.maths.unifrac.fast_tree.unifrac_matrix

All Samples(14)  |  Call(12)  |  Derive(0)  |  Import(2)

```from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from cogent.maths.unifrac.fast_tree import (count_envs, sum_env_dict,
index_envs, get_branch_lengths, index_tree, bind_to_array,
bind_to_parent_array, _is_parent_empty, delete_empty_parents,
```
```            [0,1,1],[1,1,1]])
bl = self.branch_lengths
result = unifrac_matrix(bl, m)
self.assertEqual(result, array([[0, 10/16.,8/13.],[10/16.,0,8/17.],\
[8/13.,8/17.,0]]))
#should work if we tell it the measure is asymmetric
result = unifrac_matrix(bl, m, is_symmetric=False)
```
```            [8/13.,8/17.,0]]))
#should work if the measure really is asymmetric
result = unifrac_matrix(bl,m,metric=unnormalized_G,is_symmetric=False)
self.assertEqual(result, array([[0, 1/17.,2/17.],[9/17.,0,6/17.],\
[6/17.,2/17.,0]]))
#should also match web site calculations
envs = self.count_array
bound_indices = bind_to_array(self.nodes, envs)
bool_descendants(bound_indices)
result = unifrac_matrix(bl, envs)
```

```from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from cogent.maths.unifrac.fast_tree import (count_envs, sum_env_dict,
index_envs, get_branch_lengths, index_tree, bind_to_array,
bind_to_parent_array, _is_parent_empty, delete_empty_parents,
```
```            [0,1,1],[1,1,1]])
bl = self.branch_lengths
result = unifrac_matrix(bl, m)
self.assertEqual(result, array([[0, 10/16.,8/13.],[10/16.,0,8/17.],\
[8/13.,8/17.,0]]))
#should work if we tell it the measure is asymmetric
result = unifrac_matrix(bl, m, is_symmetric=False)
```
```            [8/13.,8/17.,0]]))
#should work if the measure really is asymmetric
result = unifrac_matrix(bl,m,metric=unnormalized_G,is_symmetric=False)
self.assertEqual(result, array([[0, 1/17.,2/17.],[9/17.,0,6/17.],\
[6/17.,2/17.,0]]))
#should also match web site calculations
envs = self.count_array
bound_indices = bind_to_array(self.nodes, envs)
bool_descendants(bound_indices)
result = unifrac_matrix(bl, envs)
```