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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||||||
| 0000338 | MEGA | Calculation Error | public | 2016-12-09 07:59 | 2023-04-14 00:51 | ||||||||
| Reporter | guest | ||||||||||||
| Assigned To | |||||||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||||||
| Status | new | Resolution | open | ||||||||||
| Platform | OS | ||||||||||||
| Product Version | |||||||||||||
| Target Version | Fixed in Version | ||||||||||||
| Summary | 0000338: synonymous nucleotide substitutions | ||||||||||||
| Description | With MEGA6 I have already noticed this problem. Now I am testing the last version MEGA7 and I have noticed that the problem persists. I tested the program with 2 sequences 5 codons-long, which have one change each codon (2 synonymous and 3 non-synonymous). Nevertheless, I only obtain values for the non-synonymous substitutions. For the synonymous, I only obtain a red highlighted n/c, even for the number of differences!! | ||||||||||||
| Steps To Reproduce | sequences used: >seqA TTTAATTTTAATAAT >seqB TTCAAATTCAAAAAC Nei-Gojobori method (Number of differences) Synonymous n/c (when actually there are 3) Non-Synonymous 2 | ||||||||||||
| Tags | No tags attached. | ||||||||||||
| Attach Tags | (Separate by ",") | ||||||||||||
| First Name | Dorcas | ||||||||||||
| Last Name | Orengo | ||||||||||||
| dorcasorengo@ub.edu | |||||||||||||
| Confirm Email | dorcasorengo@ub.edu | ||||||||||||
| Attached Files | |||||||||||||
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(0000250) gstecher (administrator) 1969-12-31 17:33 |
I was not able to reproduce this bug. I suggested that the user download MEGA 3 again to ensure he is using the latest version. |
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(0000251) Nikita Vikhrev (reporter) 1969-12-31 17:33 |
He may use parsimony. Then, MEGA stops at that moment. |
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(0000268) gstecher (administrator) 1969-12-31 17:33 |
Ok, this happens using MP. This should be fixed with Koichiro\'s MP code update. |
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(0000278) gstecher (administrator) 1969-12-31 17:33 |
Yeah, this is not really a bug. He\'s just using lots of Taxa, and MEGA really doesn\'t show any progress when it\'s searching initial trees for a large number of taxa. We should probably put some sort of additional progress graphic like in WebBrowser to show that there is still activity. |
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(0000345) gstecher (administrator) 1969-12-31 17:33 |
This was fixed for 3.5 |
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Notes |
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Issue History |
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| Date Modified | Username | Field | Change |
| 2016-12-09 07:59 | guest | New Issue | |
| 2016-12-09 13:21 | gstecher | File Deleted: BwSC-3-10pct.zip | |
| 2023-01-01 16:31 | guest | Note Added: 0005947 | |
| 2023-01-01 16:47 | guest | Note Added: 0005948 | |
| 2023-01-01 18:12 | guest | Note Added: 0005949 | |
| 2023-01-01 20:40 | guest | Note Added: 0005950 | |
| 2023-01-01 21:34 | guest | Note Added: 0005951 | |
| 2023-01-02 00:24 | guest | Note Added: 0005952 | |
| 2023-01-02 03:09 | guest | Note Added: 0005953 | |
| 2023-01-02 04:21 | guest | Note Added: 0005954 | |
| 2023-01-02 04:21 | guest | Note Added: 0005955 | |
| 2023-04-14 00:51 | guest | Note Added: 0006338 | |
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Issue History |
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