EXAMPLES

Example 1.

To understand the purpose and usage of MARS please execute the following steps:

1. Upload the file ./data/10.gappy.fasta on https://www.ebi.ac.uk/jdispatcher/msa/clustalo. 
   Set the alphabet to DNA and the output format to PHYLIP. Then hit SUBMIT.

2. Inspect the produced MSA.

3. Conduct a typical run of MARS for file ./data/10.gappy.fasta using the hCED method with the following command:
	
	$ ./mars -a DNA -m 0 -i ./data/10.gappy.fasta -o ./data/10.gappy.output.fasta -q 5 -l 20 -P 1
	
	or the following command for using the branch and bound method:
	
	$ ./mars -a DNA -m 1 -i ./data/10.gappy.fasta -o ./data/10.gappy.output.fasta -l 20 -P 1

   The sequences are now refined via cyclic rotations and output in file ./data/10.gappy.output.fasta.	

4. Upload the file ./data/10.gappy.output.fasta on https://www.ebi.ac.uk/jdispatcher/msa/clustalo. 
   Set the alphabet to DNA and the output format to PHYLIP. Then hit SUBMIT.

5. Inspect the produced MSA and contrast it to the MSA produced by Step 1.