A computer program performs level-2 processing of thermal-microwave-radiance data from observations of the limb of the Earth by the Earth Observing System (EOS) Microwave Limb Sounder (MLS). The purpose of the processing is to estimate the composition and temperature of the atmosphere versus altitude from .8 to .90 km. "Level-2" as used here is a specialists f term signifying both vertical profiles of geophysical parameters along the measurement track of the instrument and processing performed by this or other software to generate such profiles. Designed to be flexible, the program is controlled via a configuration file that defines all aspects of processing, including contents of state and measurement vectors, configurations of forward models, measurement and calibration data to be read, and the manner of inverting the models to obtain the desired estimates. The program can operate in a parallel form in which one instance of the program acts a master, coordinating the work of multiple slave instances on a cluster of computers, each slave operating on a portion of the data. Optionally, the configuration file can be made to instruct the software to produce files of simulated radiances based on state vectors formed from sets of geophysical data-product files taken as input.