This server allows you to run AMAS on your own multiple sequence alignment. If you would like to run AMAS on your own computer, you can obtain the package by following the instructions on our WWW pages. You can also read the paper that describes the AMAS algorithm.
You may find the AMAS manual helpful. This describes the program and file formats.
You can try the example alignment file (in AMPS format) and corresponding "Sensible Groups" file. Click the button below to insert the example files into the input boxes.
Select the conservation threshold:
This is the most useful parameter to fiddle with. Higher numbers highlight more highly conserved positions, lower numbers highlight less conserved positions. Values between 5 and 10 are worth trying with the property tables available here; 7 is a good default starting point.
You can set some of the many AMAS options here. See the AMAS manual for details.