I'm just developing a simple desktop application. you could convert your SOLiD 5500 xsq files to csfasta and quality data using your favorite Linux desktop distribution.
Screenshots:
This is the main window, you can browse and select your xsq files clicking XSQ ==> CSFASTA+QUAL button.
Or you can select File menu then select Load SOLiD 5500 XSQ file menu.
Filter and select your XSQ files.
myXSQ ask you if you want to convert your selected XSQ files to csfasta and qual files.
you will need to configure your output directory where to save your csfasta and quality values first.
Select your Output directory.
Preview of your csfasta and quality files
myXSQ shows important information about licensing ,myXSQ is Software Libre but you will need to get an official XSQ Tools version from Applied Biosystems because I can't distribute XSQ Tools.
myXSQ will support more features.
