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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0002083 | MEGA | [All Projects] Feedback | public | 2020-06-19 10:50 | 2020-06-19 14:44 | ||||
| Reporter | guest | ||||||||
| Assigned To | gstecher | ||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||
| Status | resolved | Resolution | won't fix | ||||||
| Platform | OS | ||||||||
| Product Version | MEGA 11 (Graphical Interface version) | ||||||||
| Target Version | Fixed in Version | ||||||||
| Summary | 0002083: Problem regarding ML tree building | ||||||||
| Description | Hello Sir/Madam, I Soumila Mondal, a research scholar from Banaras Hindu University is writing to you as I am facing difficulties during tree building. Currently, I am working on a protein that bears selenocysteine (U). During ML tree construction the software pop up a window having a message unusual amino acid residue found. The residue U is so important for my study thus I can't delete it. Thus I request you to give me suggestions on this matter as soon as possible. Thanking You | ||||||||
| Tags | No tags attached. | ||||||||
| Attach Tags | (Separate by ",") | ||||||||
| First Name | SOUMILA | ||||||||
| Last Name | MONDAL | ||||||||
| soumila.bhu@gmail.com | |||||||||
| Confirm Email | soumila.bhu@gmail.com | ||||||||
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(0004482) gstecher (administrator) 2020-06-19 14:44 |
Hi Soumila, I am writing in response to your question regarding the MEGA software. Unfortunately the models used in MEGA do not support selenocysteine so the only option for analyzing the data in MEGA would be to treat those bases as ambiguous data. I think you might want to look at RAxML, Phyml, PAML, or some other software for constructing an ML tree and see if any of them support selenocysteine. -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu |
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Issue History |
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| Date Modified | Username | Field | Change |
| 1969-12-31 17:33 | user19 | Status | new => closed |
| 1969-12-31 17:33 | user19 | Resolution | open => fixed |
| 2020-06-19 10:50 | guest | New Issue | |
| 2020-06-19 14:44 | gstecher | Note Added: 0004482 | |
| 2020-06-19 14:44 | gstecher | Status | new => resolved |
| 2020-06-19 14:44 | gstecher | Resolution | open => won't fix |
| 2020-06-19 14:44 | gstecher | Assigned To | => gstecher |
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Issue History |
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