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 Hi John and all, 
In fact, I am also looking for the time alignment 
of two samples, one is the original, and another is decoded. My problem is to 
estimate the time delay caused by audio coding. 
I try a classifical estimation method, which makes 
use of envelope based cross-correlation function. That means, the envelopes of 
two samples are computed firstly, and then calculate the cross correlation 
function of these two envelopes, and then select the time length corresponding 
to the maximal correlation as the delay. 
I hope this method will help you, and if anyone has 
better approaches, please let me know, thank you very much. 
BR,  Junyong You 
TUT, Finland 
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