k-yahara
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Posts: 3
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Dear HYPHY developpers and contributors,
This is the first time to post a question to this forum. I'm graduate student in Kurume University in Japan, and make the best of HYPHY for bacterial genomics. Thank you for this great software.
This is a question about completely different results of PARRIS produced by HYPHY ver1.0 and ver2.0.
When I execute HYPHY to conduct PARRIS analysis by $ ./HYPHY my_PARRIS.bf , output of ver.1.0 was as follows
+--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+ | Model | Log Likelihood | Synonymous CV | NS Exp and CV | N/S Exp and CV | P-Value | Prm | AIC | +--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+ | discr(3), M1a | -4918.92369 | 3.18058855 | 0.17065,2.03387 | 1.10154, 2.41569 | N/A | 29| 9895.85| +--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+ | discr(3), M2a | -4908.81417 | 1.43545198 | 0.49468,2.38712 | 2.08077, 2.75454 | 0.0001529 | 32| 9881.63|
although output of ver.2.0 was as follows
########### 3x3 CLASSES ###########
+--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+ | Model | Log Likelihood | Synonymous CV | NS Exp and CV | N/S Exp and CV | P-Value | Prm | AIC | +--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+ | discr(3), M1a | -5111.29881 | 1.39897795 | 0.25228,0.00000 | 1.04456, 0.54217 | N/A | 29| 10280.60| +--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+ | discr(3), M2a | -5115.76487 | 1.51699935 | 0.22319,0.00000 | 1.56977, 0.70157 | 1.0000000 | 32| 10295.53| +--------------------+----------------+---------------+-----------------+------- -----------+-----------+-----+-----------+
Is this a bug in developmental v2.0? Is the result of v1.0 correct?
The following is the file "my_PARRIS.bf" which I used for HYPHY v1.0 and v2.0.
inputRedirect = {}; inputRedirect["01"]="Universal"; inputRedirect["02"]="1"; inputRedirect["03"]="/home/k-yahara/HYPHY/test.nex"; inputRedirect["04"]="/home/k-yahara/HYPHY/test.nex.tre"; inputRedirect["05"]="Codon Model"; inputRedirect["06"]="MG"; inputRedirect["07"]="REV"; inputRedirect["08"]="Multi"; inputRedirect["09"]="Default"; inputRedirect["10"]="Dual"; inputRedirect["11"]="Independent"; inputRedirect["12"]="Nucleotide (syn3)"; inputRedirect["13"]="PARRIS"; inputRedirect["14"]="Default"; inputRedirect["15"]="/home/k-yahara/HYPHY/test.nex.parris"; ExecuteAFile("/home/k-yahara/HYPHY/TemplateBatchFiles/PARRIS.bf", inputRedirect);
Sincerely,
Koji Yahara, Kurume University School of Medicine
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