MantisBT - MEGA | |||||
| View Issue Details | |||||
| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0000053 | MEGA | [All Projects] Feedback | public | 2016-02-17 15:41 | 2023-04-14 18:36 |
| Reporter | guest | ||||
| Assigned To | |||||
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | new | Resolution | open | ||
| Platform | Mac | OS | OS X | OS Version | 10.8 |
| Product Version | MEGA 11 (Graphical Interface version) | ||||
| Target Version | Fixed in Version | ||||
| First Name | Zain | ||||
| Last Name | Alvi | ||||
| zain.alvi@student.shu.edu | |||||
| Confirm Email | zain.alvi@student.shu.edu | ||||
| Summary | 0000053: Different Bootstrap Phylogenetic trees - Mega 6.06 vs Mega 7 | ||||
| Description | Dear Sir or Madam, I hope this reaches you well. I have been trying to re-create the same bootstrap phylogenetic tree that I created with Mega 6.06 with now Mega 7. Unfortuantely, I am not getting the same tree generated as before. I have used the same settings as before with Muscle for the alignment and the same settings in Mega for creating the Maximum Likelihood tree with 1000x bootstrap. I was wondering if you could kindly share what has changed since Mega 6.06 to cause this occur with Mega 7. I would really appreciate any insight on how to tackle this and to create the same bootstrap phylogenetic tree with Mega 7 as with Mega 6.06. I have included the settings used for both muscle alignment and phylogenetic - ML tree generation settings in additional information section. Sincerely, Zain --- zain.alvi@student.shu.edu PhD Candidate Molecular Bioscience Seton Hall University Ph: (973) 710-7149 | ||||
| Steps To Reproduce | |||||
| Additional Information | Muscle Alignment: Gap Open: -2.9 Gap Extend: 0 Hydrophobicity Multiplier: 1.2 Cluster Method (Iteration 1,2): UPGMB Clustering Method (Other Iterations): UPGMB Mind Diag Length: (lambda): 24 Tree: Analysis Analysis ------------------------ Phylogeny Reconstruction Statistical Method -------------- Maximum Likelihood Phylogeny Test Test of Phylogeny --------------- Bootstrap method No. of Bootstrap Replications --- 1000 Substitution Model Substitutions Type -------------- Amino acid Model/Method -------------------- Jones-Taylor-Thornton (JTT) model Rates and Patterns Rates among Sites --------------- Uniform rates Data Subset to Use Gaps/Missing Data Treatment ----- Partial deletion Site Coverage Cutoff (%) -------- 95 Tree Inference Options ML Heuristic Method ------------- Nearest-Neighbor-Interchange (NNI) Initial Tree for ML ------------- Make initial tree automatically (Default - NJ/BioNJ) Branch Swap Filter -------------- Strong System Resource Usage No. of Seqs : 8 No. of Sites : 77 No Of Bootstrap Reps = 1000 | ||||
| Tags | No tags attached. | ||||
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| Issue History | |||||
| Date Modified | Username | Field | Change | ||
| 2016-02-17 15:41 | guest | New Issue | |||
| 2022-12-05 06:55 | guest | Note Added: 0005879 | |||
| 2023-04-14 18:36 | guest | Note Added: 0006462 | |||