Identity is the degree of correlation between 2 un-gapped sequences, and indicates that the amino acids or nucleotides at a particular position are an exact match. What is the difference between similarity and identity?

For aligning a large number of sequences, you must have sufficient computer memory and storage. For some perspective, I can usually align ~750 sequences of 1000 nucleotides each in about an hour using MUSCLE. For instance, the sequencing program MUSCLE can usually handle large data sets with a premium on accuracy. First, you must choose an appropriate algorithm. You can align several hundred to several thousand if you wish, but there are several factors that can make this straightforward and simple or a time hog if not impossible.

MUSCLE or one of the Clustal algorithms like ClustalW. Most programs will align 3 or more sequences at a time and will require a different algorithm e.g. For comparing 2 sequences you’ll need to perform a “pairwise” alignment. You must have a minimum of 2 sequences to perform an alignment. We’re going to take a look at just the basics of sequence alignment to get you started. Whether you’re employing sequencing gels, Sanger-based methods, or the latest in pyrosequencing or ion torrent technologies, obtaining, manipulating and analyzing your sequences has never been easier. Fortunately, those of us who have learned how to sequence know that aligning sequences is a lot easier and less time consuming than creating them.

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