Software for analysis of clones - - Hamming distance/Shannon entropy etc. (Nov/30/2010 )

I am looking for some software to analyse clones for some work I am doing with quasispecies.
It has been suggested to me that I can calculate my Hamming distances (+ confidence intervals) manually but with roughly 1,000 clones to analyse, this is not appealing.
If it is the case that I have to do it manually, is from a consensus sequence that I have to calculate them?
I have been using Mega4.0 for my phylogenetic trees but this calculates only p-values for genetic distances. I have also downloaded some of Stuart Ray's freeware but must admitt that I haven't been able to give me the figures I need.
Can anyone recommend a user friendly platform for calculating Hamming distances/ Shannon entropy etc for multiple sequence alignments?
All advice much appreciated.
Dan

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