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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||||||
| 0000441 | MEGA | [All Projects] Feedback | public | 2017-04-25 02:41 | 2024-04-17 02:41 | ||||||||
| Reporter | guest | ||||||||||||
| Assigned To | |||||||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||||||
| Status | new | Resolution | open | ||||||||||
| Platform | PC | OS | Linux | ||||||||||
| Product Version | MEGA-CC 11 (command line version) | ||||||||||||
| Target Version | Fixed in Version | ||||||||||||
| Summary | 0000441: MEGA-CC is very slow when using Bootstrap | ||||||||||||
| Description | When doing Phylogeny Reconstruction, MEGA-CC is very slow when using Bootstrap in Neighbor-joining (~20s). The GUI version on MEGA is very fast (<1s) An example data containing alignments of four DNA sequences is attached. The result is: No. Bootstrap Running time(s) None 0.046 50 2.578 100 5.114 200 10.179 500 25.374 | ||||||||||||
| Steps To Reproduce | Platform: CentOS 6.9, x86_64 Data: see attached file MAO: see below =========== infer_NJ_nucleotide.mao ============= ; Please do not edit this file! If this file is modified, results are unpredictable. ; Instead of modifying this file, simply create a new MEGA Analysis Options file by using the MEGA Prototyper. [ MEGAinfo ] ver = 7160929-x86_64 Linux [ DataSettings ] datatype = snNucleotide containsCodingNuc = False MissingBaseSymbol = ? IdenticalBaseSymbol = . GapSymbol = - [ ProcessTypes ] ppInfer = true ppNJ = true [ AnalysisSettings ] Analysis = Phylogeny Reconstruction Scope = All Selected Taxa Statistical Method = Neighbor-joining Phylogeny Test = Not Applicable Test of Phylogeny = Bootstrap method No. of Bootstrap Replications = 500 Substitution Model = ==================== Substitutions Type = Nucleotide Model/Method = Jukes-Cantor model Substitutions to Include = All Rates and Patterns = ==================== Rates among Sites = Uniform Rates Gamma Parameter = Not Applicable Pattern among Lineages = Same (Homogeneous) Data Subset to Use = ==================== Gaps/Missing Data Treatment = Pairwise deletion Site Coverage Cutoff (%) = Not Applicable Has Time Limit = False Maximum Execution Time = -1 Running command: megacc -a infer_NJ_nucleotide.mao -d all.fasta -o all.nwk | ||||||||||||
| Tags | No tags attached. | ||||||||||||
| Attach Tags | (Separate by ",") | ||||||||||||
| First Name | Tao | ||||||||||||
| Last Name | Zhu | ||||||||||||
| zhutao@caas.cn | |||||||||||||
| Confirm Email | zhutao@caas.cn | ||||||||||||
| Attached Files |  all.fasta (5,760 bytes) 2017-04-25 02:41 | ||||||||||||
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| Date Modified | Username | Field | Change |
| 2017-04-25 02:41 | guest | New Issue | |
| 2017-04-25 02:41 | guest | File Added: all.fasta | |
| 2022-12-05 06:55 | guest | Note Added: 0005877 | |
| 2023-04-14 18:36 | guest | Note Added: 0006464 | |
| 2024-04-17 02:40 | guest | Tag Attached: mega | |
| 2024-04-17 02:41 | guest | Tag Detached: mega | |
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