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Notes |
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(0002952)
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user614
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1969-12-31 17:33
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Hello Hiroko,
I am writing in response to the bug report you recently submitted to the MEGA bug tracker regarding a calculation error when doing the codon by codon test of selection with Hyphy. I have not been able to duplicate the error. Could you send me the alignment file used for the analysis as well as the Excel output file? Also, could you tell me what settings were used for the analysis? This would really help me to understand the error. Thanks in advance.
Best regards,
Glen Stecher |
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(0002955)
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user614
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1969-12-31 17:33
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Hi Hiroko,
Thanks for sending those files. I am able to duplicate the error and it seems that the indels that start at position 113 and span 2 codons are causing problems for MEGA. The next release of MEGA will have this issue fixed but in the meantime, the workaround is to remove from the alignment those two codons which are spanned by the indels. For your convenience I have attached the alignment file with those two codons removed. Thanks for finding this bug.
Best regards,
Glen Stecher |
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(0002973)
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user614
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1969-12-31 17:33
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had to rewrite the entire data preparation for hyphy analysis. Also had to fix several problems with the results export. |
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(0006344)
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guest
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2023-04-14 00:52
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