So I need to make an alignment using secondary structure for gap penalties. I have found that Clustal is suppose to be able to do this but I try to follow their instructions (http://www.bugaco.com/bioinf/ClustalW/helpB.html) and it does not even read the secondary structure correctly specifically the "." are completely ignored.
If anyone has gotten this to work for them please let me know what you did.
Josh
P.S. Also open to any other program that has this functionality.
If anyone has gotten this to work for them please let me know what you did.
Josh
P.S. Also open to any other program that has this functionality.
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