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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0001148 | MEGA | Distance Data Explorer | public | 2019-03-12 00:09 | 2019-03-18 08:18 | ||||
| Reporter | guest | ||||||||
| Assigned To | gstecher | ||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||
| Status | resolved | Resolution | no change required | ||||||
| Platform | PC | OS | Windows | ||||||
| Product Version | |||||||||
| Target Version | Fixed in Version | ||||||||
| Summary | 0001148: With the increase in the number of sequences, the pairwise distances are different.(MEGA 7) | ||||||||
| Description | While I was calculating the pairwise distances of a FASTA file which including 44 families and 870 sequences, I found if I calculate every family separately, the pairwise distances of same sequences may be different. For example, the distance between “Cinara pilicornis|ACEA154-14” and “Cinara pilicornis|GBMHH3689-14” is 0.036 in “Aphididae-14.fas” (including 44 families and 870 sequences) and 0.064 in ”Cinara pilicornis.fas” (only one family, 30 sequences). | ||||||||
| Steps To Reproduce | Input Data(Data Type: "Nucleotide Sequences" ) Select Genetic Code ("Standard") Compute Pairwise Distances(Variance Estimation Method:"None";Substitutions type:"Nucleotide";Model/Method:"Kimura 2-parameter model") Export to CSV formatted file(Export Type:"Column") | ||||||||
| Additional Information | MEGA Version 7.0.26 | ||||||||
| Tags | No tags attached. | ||||||||
| Attach Tags | (Separate by ",") | ||||||||
| First Name | Zhentao | ||||||||
| Last Name | Cheng | ||||||||
| zhentao.cheng0123@gmail.com | |||||||||
| Confirm Email | zhentao.cheng0123@gmail.com | ||||||||
| Attached Files |  Upload File.rar (87,639 bytes) 2019-03-12 00:09 | ||||||||
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(0004207) gstecher (administrator) 2019-03-18 08:18 |
Hi Zhentao, I am writing in response to your question regarding the MEGA software. The difference in pairwise distances you reported happen because you are using the 'Complete Deletion' option so the data subset used is different between the files. You can use the 'Pairwise Deletion' option if you expect the distances to be the same when using the two input files. -- 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 |
| 2019-03-12 00:09 | guest | New Issue | |
| 2019-03-12 00:09 | guest | File Added: Upload File.rar | |
| 2019-03-18 08:04 | gstecher | Note Deleted: 0001059 | |
| 2019-03-18 08:04 | gstecher | File Deleted: ANTcrustaceans_Complete5.mas | |
| 2019-03-18 08:18 | gstecher | Note Added: 0004207 | |
| 2019-03-18 08:18 | gstecher | Status | new => resolved |
| 2019-03-18 08:18 | gstecher | Resolution | open => no change required |
| 2019-03-18 08:18 | gstecher | Assigned To | => gstecher |
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Issue History |
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