Examples of standard AMAS usage:

    Multiple property table with histogram 8 units high, ignoring one gap with
    shading selected considering positive and negative property conservation:

        amas -sg1h8f   sh2.aln intra.pt sh2.sg     7 4 general.h/sh2gh

    Multiple property table with pair scores, ignoring one gap with
    shading selected, considering positive and negative property conservation:

        amas -sg1f     sh2.aln intra.pt sh2.sg     7 4 general.p/sh2gp

    Charge property table with pair scores, ignoring one gap with shading
    selected, considering positive property conservation only:

        amas -sg1fn    sh2.aln ch.pt    sh2.sg     2 4 charge.p/sh2cp

    Charge property table with histogram 12 units high, ignoring one gap with
    shading selected, considering positive property conservation only:

        amas -sg1h12fn sh2.aln ch.pt    sh2.sg     2 4 charge.h/sh2ch


Example including additional information:

    Multiple proeprty table considering positive and negative property 
    conservation.   Each residue type must have a minimum occupancy of
    15% of a sub-group in order to be considered in the conservation 
    calculation.   One gap may be ignored, a histogram of standard height 
    (10 units) is drawn and shading is selected:

        amas -a15g1hcf sh2.stb intra.pt sh2.str.sg 7 5 structure/sh2.stb
