Need help to edit multiple sequence alignment?

[AntonioRFranco]

The inclusion of "X" into a MSF file is the consequence of having applied a filter for low complexity sequences present into your protein

You can make the choice of turning on or off such as filtering before the actual aligment is done

[GenoMax]

You should tell us how or it did not happen

On a serious note MEGA or ClustalW should have been able to do it.

[ashmi]

I did it

[ashmi]

I have a large concatenated protein multiple sequence alignment. One of the species have many undetermined 'X' amino acid. Such column will probably not add much phylogenetic signal so I want to remove all such column (that contain any X) from my alignment file.