Can you suggest any software?
In most cases yes
Check the following links
http://bioinformatics.oxfordjournals.org/content/early/2012/10/10/bioinformatics.bts609.full.pdf
http://bib.oxfordjournals.org/content/early/2013/01/21/bib.bbs086.full.pdf+html
Is it for a functional gain or a nonsense anatomical variation
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