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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||||||
| 0000031 | MEGA | [All Projects] Suggestion | public | 2016-02-05 06:44 | 2016-02-05 15:01 | ||||||||
| Reporter | guest | ||||||||||||
| Assigned To | gstecher | ||||||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||||||
| Status | assigned | Resolution | open | ||||||||||
| Platform | PC | OS | Linux | ||||||||||
| Product Version | MEGA-CC 11 (command line version) | ||||||||||||
| Target Version | Fixed in Version | ||||||||||||
| Summary | 0000031: Genetic codes | ||||||||||||
| Description | Hi I am using the command line version on some mitochondrial sequences and I want to test for selection using Z-test but I have a problem because I can't change the genetic code on megaproto, and I am getting stop codons in my sequences. Is there a way to manipulate the file or the .mao file so it can change to mitochondrial genetic code? Thanks in advance | ||||||||||||
| Tags | No tags attached. | ||||||||||||
| Attach Tags | (Separate by ",") | ||||||||||||
| First Name | Themis | ||||||||||||
| Last Name | Giannoulis | ||||||||||||
| themisgia@hotmail.com | |||||||||||||
| Confirm Email | themisgia@hotmail.com | ||||||||||||
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(0003590) gstecher (administrator) 2016-02-05 15:01 |
Hi Themis, I am writing in response to the question you recently posted to the MEGA bug tracker regarding how to set the genetic code table for the z-test of selection analysis. Thanks for the feedback. We will fix the bug you found soon. In the meantime, I think you can work around the problem as follows: Add a couple of lines for the genetic code table to the .mao file as in the attached example. If you need a different code table from the one in the example then: open megaproto select coding data select some other analysis (like Phylogeny->Construct/Test Maximum Likelihood Tree...) set the Substitution Type to Amino Acid select the desired genetic code table save that mao file open that mao file in a text editor and copy the two code table lines from that file paste the two code table lines into your .mao file for the z-test -- Best regards, Glen Stecher |
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Issue History |
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| Date Modified | Username | Field | Change |
| 2016-02-05 06:44 | guest | New Issue | |
| 2016-02-05 15:01 | gstecher | Assigned To | => gstecher |
| 2016-02-05 15:01 | gstecher | Status | new => assigned |
| 2016-02-05 15:01 | gstecher | Note Added: 0003590 | |
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