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Model data from the latest NOAA WAVEWATCH III® runs is available in GRIB (GRIdded Binary) format on the NCEP NOMADS GDS/DODS data server, and the NCEP Central Operations Production FTP server, at the following URLs:
The operational data file format is GRiB (GRIdded Binary). Additional information on the use of GRiB at NCEP is available here.
To work with WAVEWATCH III® GRiB, any standard tools which read GRiB will work. One such tool is the freely available wgrib2 utility. The wgrib2 home page and software is here.
For analyzing the model data in MATLAB® we recommend the NCTOOLBOX for MATLAB. NCTOOLBOX can read NetCDF, OPeNDAP, HDF5, GRIB, GRIB2, HDF4 and many (15+) other file formats. The complete list of formats is available here.