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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0006717 | MEGA | Alignment Explorer | public | 2025-03-07 01:01 | 2025-03-07 01:01 |
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| Reporter | guest | |
| Assigned To | | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | new | Resolution | open | |
| Platform | Mac | OS | OS X | |
| Product Version | MEGA-CC 10 and prior | |
| Target Version | | Fixed in Version | | |
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| Summary | 0006717: bugs of function MUSCLE Codon Alignment |
| Description | MEGA version: 10.2.6
System: MacOS 15.3.1
When I use MEGA GUI to produce the ".mao" file with Vertebrate Mitochondrial codon table for the MUSCLE Codon Alignment function, and then use the command line (megacc -a muscle_align_coding.mao -d ATP6.fas -o ATP6) to align my sequences, I have got warnings "Stop Codon(s) are found in the translated sequences. Is the correct genetic code selected?", as well as lots of "*** WARNING *** Invalid character '*' in FASTA sequence data, ignored". Finally, I found that the GeneticCodeTable in .mao file still the "Standard", although the Genetic Code was set to Vertebrate Mitochondrial. |
| Additional Information | I have got the same warnings when I use the MUSCLE Codon Alignment function using MEGA GUI.
Besides, I was use a MacOS with ARM-based M-series chips, the MEGA GUI does not compatible with it well. I am really looking forward to the update for M-series chips of MacOS. |
| Tags | No tags attached. |
| Attach Tags | (Separate by ",")
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|
| First Name | Shiwu |
| Last Name | Dong |
| Email | dongshiwu2017@126.com |
| Confirm Email | dongshiwu2017@126.com |
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| Attached Files |  muscle_align_coding.mao (1,750 bytes) 2025-03-07 01:01
 ATP6_summary.txt (2,946 bytes) 2025-03-07 01:01 |
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