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Old 07-24-2014, 12:05 AM   #2
Matt Kearse
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Location: New Zealand

Join Date: Mar 2014
Posts: 20
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Geneious can do it although it's commercial software. There is probably some free software out there to do it, but I'm not aware of any.

A year or two ago I heard (and this might be wrong) that Geneious was the only software that correctly calls phased amino acid effects when for example only the first and third position in a codon have SNPs. You can watch a 30 second demo of this at https://www.youtube.com/watch?v=IOGmxjK3f_4#t=2m57s
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