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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||||||
| 0006610 | MEGA | Tree Explorer | public | 2024-07-15 10:07 | 2024-07-15 10:07 | ||||||||
| Reporter | guest | ||||||||||||
| Assigned To | |||||||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||||||
| Status | new | Resolution | open | ||||||||||
| Platform | PC | OS | Windows | ||||||||||
| Product Version | MEGA 11 (Graphical Interface version) | ||||||||||||
| Target Version | Fixed in Version | ||||||||||||
| Summary | 0006610: Maximum likelihood bootstrap freeze | ||||||||||||
| Description | Running nucleotide data through the phylogeny option > maximum likelihood analysis with bootstrapping at 500 bootstrap freezes very quickly after beginning. I've closed and attempted to rerun the data five separate times and when the analysis doesn't outright freeze on a bootstrap indefinitely, the entire program will stop responding and freeze. | ||||||||||||
| Steps To Reproduce | From the plant bioinformatics lab " 1. Start MEGA and load the aligned DNA sequence in MEGA format as per Step 2 on Page 4 (File > Open a Recently Used File and choose the aligned DNA sequences in MEGA format that you prepared earlier in this lab). 2. Under Analysis > Phylogeny > Construct/Test Maximum Likelihood Tree… set the Phylogeny Test / Test of Phylogeny to Bootstrap, with 500 replications, and leave all the other settings at their default values (see Appendix 2 for defaults; increasing the number of threads might speed up the analysis, however). Click Compute to start the analysis. 3. Wait quite a bit longer than you did with the Neighbour Joining analysis. As explained in the mini-lecture, a lot more computation is used in the Maximum Likelihood algorithm. The progress bar will show the extent to which your analysis is complete. Once the analysis is done, the Tree Viewer will open and display the resultant tree. Bioinformatic Methods I Lab 4 Copyright © 2024 by D.S. Guttman and N.J. Provart 13 4. You can now manipulate and play with the tree just as you did previously. " These are the steps I used to reach the issue. | ||||||||||||
| Tags | No tags attached. | ||||||||||||
| Attach Tags | (Separate by ",") | ||||||||||||
| First Name | David | ||||||||||||
| Last Name | Geiger | ||||||||||||
| dgeiger3@charlotte.edu | |||||||||||||
| Confirm Email | dgeiger3@charlotte.edu | ||||||||||||
| Attached Files |  bioinfomethods1_labs_Lab3,4_sequences_DNA_aligned.meg (20,619 bytes) 2024-07-15 10:07 | ||||||||||||
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| Date Modified | Username | Field | Change |
| 2024-07-15 10:07 | guest | New Issue | |
| 2024-07-15 10:07 | guest | File Added: bioinfomethods1_labs_Lab3,4_sequences_DNA_aligned.meg | |
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