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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0000319 | MEGA | [All Projects] Feedback | public | 2016-11-24 14:42 | 2016-11-28 14:17 | ||||
| Reporter | guest | ||||||||
| Assigned To | gstecher | ||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||
| Status | resolved | Resolution | fixed | ||||||
| Platform | OS | ||||||||
| Product Version | MEGA 11 (Graphical Interface version) | ||||||||
| Target Version | Fixed in Version | ||||||||
| Summary | 0000319: Default settings for protein alignment have changed? | ||||||||
| Description | Dear Profs. Kumar and Tamura, I have my bioinformatics students use MEGA for alignments. In updating the lab for this year to use MEGA7, I noticed that the defaults for protein sequence alignments using ClustalW have changed: for Pairwise/Multiple Alginments the Gap Opening penalty is now 10, instead of 1 in MEGA6. Is this true? Or is MEGA tapping in to a config file from my MEGA6 install? A "Restore Defaults" button would be nice to have in future versions! Thanks, Nick | ||||||||
| Tags | No tags attached. | ||||||||
| Attach Tags | (Separate by ",") | ||||||||
| First Name | Nicholas | ||||||||
| Last Name | Provart | ||||||||
| nicholas.provart@utoronto.ca | |||||||||
| Confirm Email | nicholas.provart@utoronto.ca | ||||||||
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(0003711) gstecher (administrator) 2016-11-28 14:17 |
Hi Nicholas, I am writing in response to your question regarding the MEGA software. The default gap opening penalty for ClustalW protein sequence alignment in both MEGA6 and MEGA7 is 10. However, when you change it to something else, MEGA will remember the new value the next time ClustalW alignment is requested. It seems that at some point, your MEGA6 install was run with ClustalW alignment with a gap opening penalty of 1 and then MEGA6 saved that information. And yes, we will try to add a 'reset defaults' option in the future. -- 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 |
| 2016-11-24 14:42 | guest | New Issue | |
| 2016-11-28 14:17 | gstecher | Note Added: 0003711 | |
| 2016-11-28 14:17 | gstecher | Status | new => resolved |
| 2016-11-28 14:17 | gstecher | Resolution | open => fixed |
| 2016-11-28 14:17 | gstecher | Assigned To | => gstecher |
| 2016-12-01 13:09 | gstecher | Relationship deleted | 0000322 |
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Issue History |
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