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HYPHY Package >> HyPhy feedback >> Codon Freqs Models corresp. btw HYPHY and PAML http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1123168806 Message started by avilella on Aug 4th, 2005 at 8:20am |
Title: Codon Freqs Models corresp. btw HYPHY and PAML Post by avilella on Aug 4th, 2005 at 8:20am
Dears,
I'm trying to assess the dN and dS by-branch results I get from the same data using the Local/free-ratios model under HYPHY/PAML under the different available models of codon frequencies for each program. I have tried: HYPHY ----- MG94CUSTOM(HKY85) GY94 GY94W9 MG94 MG94W9 PAML ---- CodonFreq = 0 # 1/61 each CodonFreq = 1 # F1x4 CodonFreq = 2 # F3x4 CodonFreq = 3 # Fcodon CodonFreq = 4 # F1x4MG CodonFreq = 5 # F3x4MG I would like to confirm which methods in HYPHY can compare to which ones in PAML. For example: Are this models comparable? GY94 = F1x4 GY94W9 = F3x4 MG94 = F1x4MG MG94W9 = F3x4MG Which would be similar to Fcodon? And "1/61 each"? I understand that the same models under both programs should give me the same or similar results on the same dataset, while different models in one program should give more different results in the other program. Right now, it seems that the results of F3x4MG are much more similar to the results of MG94CUSTOM, rather than to those of MG94W9... Looking forward, Bests, Albert. |
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