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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> IUPAC symbols for ambiguous nucleotides http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1324377218 Message started by Lillian on Dec 20^th, 2011 at 2:33am

Title: IUPAC symbols for ambiguous nucleotides
Post by Lillian on 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?

Title: Re: IUPAC symbols for ambiguous nucleotides
Post by Sergei on 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

Title: Re: IUPAC symbols for ambiguous nucleotides
Post by Lillian on Dec 20^th, 2011 at 6:24pm

Hi Sergei,

Thank you so much!

Best regards,

Lillian