JProfileGrid is a java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. ProfileGrids are a new paradigm for concisely representing multiple sequence alignments for viewing and analysis.

For a protein sequence, a ProfileGrid matrix contains positional amino acid counts highlighted according to the frequency of the characters in the alignment.

JProfileGrid provides both command-line support and a graphical user interface. Please see the documentation files for a full description of the functionality of this software and the options available.

If JProfileGrid is not already on your Bio-Linux system, you can easily install it using a graphical package management tool such as the Ubuntu Software Centre - just search for jprofilegrid. Otherwise, you can type the following commands:
sudo apt-get update
sudo apt-get install bio-linux-jprofilegrid

References:
A.I.Roca, A.E.Almada, and A.C.Abajian, ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family, (2008) BMC Bioinformatics 9: 554