As per JB's suggestions I have created a concatenated alignment of all columns which have no gaps (from all proteins). This results in an alignment of ~1289 columns and 624 sequences (since I need to make sure all proteins are present).
Now I'm using phylip to create a tree out of these sequences ... however, this seems very slow going. Its been ~50 minutes and its only loaded 1/3rd of the sequences of the FIRST of 100 trees. I'll let it go for most of the day but this might be a little too extreme.
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