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# Make a neighbor joining tree

Section author: Gavin Huttley

An example of how to calculate the pairwise distances for a set of sequences.

    >>> from cogent import LoadSeqs
    >>> from cogent.phylo import distance, nj

Import a substitution model (or create your own)

    >>> from cogent.evolve.models import HKY85

Load the alignment.

    >>> al = LoadSeqs("data/long_testseqs.fasta")

Create a pairwise distances object calculator for the alignment, providing a substitution model instance.

    >>> d = distance.EstimateDistances(al, submodel= HKY85())
    >>> d.run()

Now use this matrix to build a neighbour joining tree.

    >>> mytree = nj.nj(d.getPairwiseDistances())

We can visualise this tree by `print mytree.asciiArt()`, which generates the equivalent of:

                        /-Human
              /edge.0--|
             |          \-HowlerMon
             |
    -root----|          /-NineBande
             |-edge.1--|
             |          \-DogFaced
             |
              \-Mouse

We can save this tree to file.

    >>> mytree.writeToFile('test_nj.tree')

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