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cogent.align.weights.util.DNA_ORDER

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```from cogent.parse.tree import DndParser
from cogent.util.array import hamming_distance
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
```
```            char_order=PROTEIN_ORDER
else: #need DNA_order
char_order=DNA_ORDER

print "===========ALIGNMENT=============="
```

```from cogent.parse.tree import DndParser
from cogent.util.array import hamming_distance
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
```
```            char_order=PROTEIN_ORDER
else: #need DNA_order
char_order=DNA_ORDER

print "===========ALIGNMENT=============="
```

```from cogent.core.sequence import DnaSequence, RnaSequence
from cogent.core.moltype import DNA, RNA
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
```

```from cogent.core.sequence import DnaSequence, RnaSequence
from cogent.core.moltype import DNA, RNA
from cogent.align.weights.util import Weights, number_of_pseudo_seqs,\
pseudo_seqs_exact, pseudo_seqs_monte_carlo, row_to_vote, distance_matrix,\
eigenvector_for_largest_eigenvalue, DNA_ORDER,RNA_ORDER,PROTEIN_ORDER,\
```

```from cogent.core.alignment import Alignment
from cogent.core.profile import Profile
from cogent.align.weights.util import DNA_ORDER, PROTEIN_ORDER
from cogent.align.weights.methods import VA, VOR, mVOR, pos_char_weights, PB,\
SS, ACL, GSC, _clip_branch_lengths, _set_branch_sum, _set_node_weight
```

```from cogent.core.alignment import Alignment