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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.
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I did it
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You should tell us how or it did not happen
On a serious note MEGA or ClustalW should have been able to do it.Comment
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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 doneComment
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