[Biopython] generate phylogenetic tree

[john fernando]

Hi,

first off, I am very new to the bioinformatics/biopython world so this may come as a naive question, so I apologize in advance.

I extracted some sequences of PDB, aligned them using BLOSUM62 and have "scores".

I was wondering if anyone can give tips/advice on I can set about generating a phylogenetic tree of the results to graphically show the clusters of similar sequences?

I want to do this for my 'own' substitution matrix (next step).

I am asking not necessarily code but more tools that people have used that can do this using the "scores" I have calculated. 
Thank you,
John

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