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IUPAC symbols for ambiguous nucleotides (Read 2219 times)

Lillian YaBB Newbies Offline Feed your monkey! Posts: 5	IUPAC symbols for ambiguous nucleotides Dec 20^th, 2011 at 2:33am There are several sequences with some IUPAC symbols for ambiguous nucleotides, e.g. R, W, and so on, instead of A, T, C, G, in my alignment file. Could any one tell me whether these ambiguous codes are accepted by the HyPhy positive selection analyses? And do these codes affect final results?
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: IUPAC symbols for ambiguous nucleotides Reply #1 - Dec 20^th, 2011 at 10:54am Hi Lillian, Yes, they are accepted as partially missing data (see Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to Login for an example). Unless your alignment has unusually many ambiguous characters, I would expect the effect to be minimal. Best, Sergei
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Lillian YaBB Newbies Offline Feed your monkey! Posts: 5	Re: IUPAC symbols for ambiguous nucleotides Reply #2 - Dec 20^th, 2011 at 6:24pm Hi Sergei, Thank you so much! Best regards, Lillian
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