HoKAlign is a GUI under Windows for several free command line driven sequence alignment programs. Currently supported programs
1. ClustalW (GUI: ClustalX 2)
2. ClustalW2 (GUI: ClustalX 1)
3. Muscle (versions 3.6 and 3.7)
4. MAFFT (supported, the source for Cygwin is stored in the subfolder \scr)
5. T-Coffee
6. KAlign
7. DiAlign
8. Prank (GUI: Prankster)
9. ProbCons
10. Amap
11. ProDA
12. PCMA
13. POA

How to install
1. Unpack the files form the Zip file while keeping the folder structur. C:\Program Files\HoKAlign\ would be a good place.
2. Create a shortcut to the file HoKAlign.exe. Your desktop would be a good place to place this shortcut.
3. Java is necessary to run ReadSeq and ATV (Archaeopteryx). ReadSeq or ClustalX are used for all programs that can not read or write MSF files (e.g. Muscle). So you should have installed Java.
4. If you want to use MAFFT you must have installed Cygwin. After that you have to install the MAFFT package, stored in the /scr subfolder.

The license of this software is Freeware, you can free download and free use this calculator software.