The hierarchical conservation analysis algorithm is implemented in the computer program AMAS (Analysis of Multiply Aligned Sequences) written in ANSI-C. AMAS can generate commands for the ALSCRIPT program [Barton, 1993], which will automatically shade, box and colour a multiple alignment according to the identified conservation patterns. AMAS and ALSCRIPT have been used successfully on a number of Unix platforms. If the graphical display options are required, then a PostScript printer or interpreter is required.