The format for .air files is identical for AIR 2.0 through AIR 5.x, so these files can be used interchangeably. The format for .warp files has been changed in AIR 5.x. The current version of AIR can read .warp files from earlier versions, but the reverse is not true.

All of the AIR 2.0 and AIR 3.0 commands are available in AIR 5.x, and efforts have been made to assure that commands syntax is unchanged. However, certain changes have proved too awkward to avoid:

• In the program alignlinear, the -w flag is no longer suppported.
• In the program align_warp, the -f flag must be followed by a .warp file name, not an ASCII text file and the -g flag is no longer supported.
• In the program combine_warp, the use of 'null' to replace one of the .air files is no longer supported and no longer needed due to greater flexibility of that program.
• In the program zoomer, the use of 'y' to grant permission to overwrite a pre-existing file is supported only so long as no new options are used, but this usage should be avoided in the future.