[Biopython] Custom Distance Matrices using Custom Scoring Matrices

[Willis, Jordan R]

Hello,

I think my solution is to use a neighbor joining from the PHYLIP package. You can define distance matrices yourself, which I will write using biopython, but I don't think that it has been done before. If I get something nice and stable, I will contribute to the devel branch of biopython.

Jordan

On May 31, 2013, at 4:15 PM, "Willis, Jordan R" <jordan.r.willis at Vanderbilt.Edu> wrote:

> 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
> 
> 
> 
> 
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