[Biopython] User Defined Scoring Matrix

[Willis, Jordan R]

Hello,

Since I'm not sure which tool to exactly use, I will defer to the biopython community since odds are I will be using it. I'm trying to produce a multiple sequence alignment with a user defined scoring matrix. When I look at Clustalw, there is an option to put in such a matrix, and the help indicates that this should be in "blast" format. When I search for blast format, they indicate that this is hard coded into the software. 

My end goal is to produce a phylogeny tree using this PSSM, but I have no idea how to input this into ClustalW or any multiple sequence alignment software. I don't really care which software to use, which wrappers, or how I have to do it.I have used biopython to produce this matrix, so I thought it would be relatively easy to implement it in any multiple sequence alignment software. 

I'm not having very good luck and any help would be must appreciated.

Jordan