-# Creates a new file named "outfile.aln" and writes
-# multiple sequence alignment 'align' to it in clustal format.
-File.open('outfile.aln', 'w') do |f|
- f.write(align.output(:clustal))
+# Other formats
+File.open('outfile.clustal', 'w') do |f|
+ f.write(msa.output(:clustal))
+end
+File.open('outfile.phylip', 'w') do |f|
+ f.write(msa.output(:phylip))
+end
+File.open('outfile.phylipnon', 'w') do |f|
+ f.write(msa.output(:phylipnon))
+end
+File.open('outfile.msf', 'w') do |f|
+ f.write(msa.output(:msf))