There is a newer version that calculates normal, overlapping, modified and times Allan deviations in one function: http://www.mathworks.com/matlabcentral/fileexchange/26659-allan-v3-0
allan.m calculates the Allan deviation of a time domain signal. It is intended for stability analysis of frequency data. Data sets with rate or time stamp information are handled.
Enhanced performance for rate in comparison to allan.m v1.61 (by M.A. Hopcroft, file ID 13246) by preallocating memory space. No changes for time stamp.
For long time series, the enhancement gets more significant.
Motivation: Calculate Allan variance for long time series with high sample rates.
Sample data available at www.nbi.dk/~czerwin/files/allan.zip
Comments by John D'Errico (Oct 14, 2008) are incorporated.