Studies evaluating multiple sequence alignment methods

If you are doing a study evaluating methods for multiple sequence alignment methods, you will typically have "reference alignments" and want to compare estimated alignments to these reference alignments. You will need to produce unaligned versions of your aligned sequences; i.e., you will need to remove gaps from the file. One possible command to remove the gaps from the alignment is: sed 's/-//g' alignment_file > unaligned_file Learn more here: http://www.theunixschool.com/2014/08/sed-examples-remove-delete-chars-from-line-file.html You will also need to compare estimated alignments to the reference alignments. See FastSP.