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
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