However, it has nice graphical user interface, it displays information on the level of similarity, and it uses color in the alignment. Especially for amino acids the use of color greatly enhances the ability to recognize conservative replacements. ClustalX is available for different platforms at the ebi's ftp site . Clustal reads and writes most formats used by different programs. It also reads aligned sequences.
Some programs require specialized formats.
You can use a text editor like MSWord to get your alignment into the desired format, but things are certainly much easier, if you start out with a format close to the desired one. Often you do not want to use the complete alignment, but only those portions which are sufficiently conserved. Although the different lines in the resulting alignment have different lengths, clustalw reads in the aligned sequences correctly, and you can output the shortened sequences in any desired format you want. For information on mathematical background of alignment algorithms visit Lectures by Dr. Michael Zuker . ClustalX manual is available here .