[Biopython] Custom Distance Matrices using Custom Scoring Matrices

[Willis, Jordan R]

Hello Bio,

I know I asked something like this a while ago but didn't really know what I needed to do. Now I think I know exactly the path, however the solution is unclear.

The goal is to compare sequences all of the same length and view them in a dendrogram. In one tree I would like it to be scored with something simple like a PAM250 matrix. In another dendrogram, I would like the tree to be scored with my own custom position-specific scoring matrix.

So it looks like I can use a neighbor-joining method using a distance matrix where the distance matrix will be all my sequences scored against each other using either the PAM250 or my custom matrix.

Now, does Biopython have the means to do this? I can quickly write a method to score all my sequences against each other using PAM250 or my PSSM and store it in some sort of dictionary. Can I then convert that dictionary to a distance matrix to be used in neighbor joining? Is there a method to write out a newick tree using neighbor joining? Should I even be using Biopython? 

Thanks so much!

Jordan