*Free shift (or semi-global) alignments will ignore gaps at the beginning and end of the sequence, while Global alignments try to consider all positions.
Use Free shift alignments when some of the sequences are terminally truncated. Local alignments (such as BLAST) are useful for
finding short stretches of homology and are useful for finding sequence overlap or detecting a short internal sequence stretches that
are shared.
http://www.uoguelph.ca/plant/depttools/dnaanalysis.htm
www.cs.ecu.edu/hochberg/spring2006/LocalAlign.pdf
birg.cs.wright.edu/text/Ch2.ppt
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