[BioPython] Bio.Cluster - Howto, Documentation, exporting results

[Renato Alves]

Hi,

I'm having some troubles understanding how to export data processed 
using Bio.Cluster.distancematrix and Bio.Cluster.treecluster .

I don't read the data from files, so I don't understand if DataFile 
class is what I need, and if it is, how do I  make use of it.

Additionally, as of BioPython-1.44, there are a couple of things 
mentioned in the documentation that are not available in Bio.Cluster.
One of those is the Bio.Cluster.read function. I don't know if this is 
because it was not yet in BioPython-1.44 or if the documentation is 
outdated.

The cookbook doesn't help either since there is nothing there regarding 
Bio.Cluster.

What I'm trying to do is to calculate the distances between some 
multidimensional vectors and then cluster them. I managed to do that, 
but then I don't know what to do with the Tree object I get. It's also 
not obvious how do I keep track of which values in the Tree object 
correspond to which entries in the distance matrix or in the original data.

So the questions are:

Is it possible to pass text in the original data so that it is used as 
some sort of identifying header in later operations?

How can I export the Tree object to something like the treeview format 
mentioned in the documentation?

Is there any way to visualize the tree directly using ASCII or something 
more graphical?

Thanks

Renato Alves