pepwindowall produces a set of superimposed Kyte & Doolittle hydropathy plots from an aligned set of protein sequences.

Here is a sample session with pepwindowall:

% pepwindowall globin.msf -gxtitle="Base Number" -gytitle="hydropathy"
Displays protein hydropathy of a set of sequences
Graph type [x11]:

Mandatory qualifiers:

[-msf] (seqset)

File containing a sequence alignment.

[-graph] (xygraph)

Graph type.

Optional qualifiers:

-datafile (datafile)

Nakai database file.

-length (integer)

Window size.