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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0002625 | MEGA | Tree Explorer | public | 2021-03-06 20:28 | 2021-03-12 09:35 | ||||
| Reporter | guest | ||||||||
| Assigned To | gstecher | ||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||
| Status | resolved | Resolution | won't fix | ||||||
| Platform | Mac | OS | OS X | ||||||
| Product Version | MEGA 11 (Graphical Interface version) | ||||||||
| Target Version | Fixed in Version | ||||||||
| Summary | 0002625: the phylogenetic tree can not show up once miinimize it | ||||||||
| Description | After I minimized the phylogenetic tree, I can not reopen it again in the main window, but the other windows still can be opened through the main window as shown in the attached image. | ||||||||
| Tags | No tags attached. | ||||||||
| Attach Tags | (Separate by ",") | ||||||||
| First Name | Yaohui | ||||||||
| Last Name | Li | ||||||||
| lvhailiyaohui@163.com | |||||||||
| Confirm Email | lvhailiyaohui@163.com | ||||||||
| Attached Files |  main window.jpg (189,657 bytes) 2021-03-06 20:28 | ||||||||
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Notes |
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(0002026) Nikita Vikhrev (reporter) 1969-12-31 17:33 |
In the Newick format, square brackets are reserved for comments as the definition. Since there is no branch length for the exterior branches, the 1.0 values for the interior branches are recognized as the confidence value "100", which is a frequently used way in other softwares like MyBayes. There is no way to distinguish them all automatically. Or, should we support Newick format for each program? |
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(0002034) user19 1969-12-31 17:33 |
In the help documentation, we provide an example where we have confidence values in the square brackets. Using an example file which has it's confidence values in square brackets, MEGA reads it in just fine. The problem appears to be that we incorrectly identify the newick tree to be in PAUP format, where if we identified it as Phylip format everything works fine. (Calling ConvertPhylipFormat instead of ConvertPAUPFormat) I'm looking further into what causes the file to be identified as PAUP rather than Phylip. |
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(0002035) Nikita Vikhrev (reporter) 1969-12-31 17:33 |
Hi, Dan. The issue is the branch lengths incorrectly described. If all ":1.0"s given to interior branches are to be recognized as branch lengths, they should be given to exterior branches too. So, if you eliminate all ":1.0"s, the tree is shown without problem. Try it. |
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(0002040) user19 1969-12-31 17:33 |
Sent the user an email explaining the problem. Will reopen this if there is need to. |
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(0004562) gstecher (administrator) 2021-03-12 09:35 |
MEGA7 is no longer supported so we won't fix this |
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Notes |
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Issue History |
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| Date Modified | Username | Field | Change |
| 1969-12-31 17:33 | Nikita Vikhrev | Note Added: 0002026 | |
| 1969-12-31 17:33 | user19 | Note Added: 0002034 | |
| 1969-12-31 17:33 | Nikita Vikhrev | Note Added: 0002035 | |
| 1969-12-31 17:33 | Nikita Vikhrev | Note Edited: 0002035 | |
| 1969-12-31 17:33 | user19 | Note Added: 0002040 | |
| 1969-12-31 17:33 | user19 | Status | new => resolved |
| 1969-12-31 17:33 | user19 | Resolution | open => fixed |
| 1969-12-31 17:33 | user19 | Assigned To | => user19 |
| 2021-03-06 20:28 | guest | New Issue | |
| 2021-03-06 20:28 | guest | File Added: main window.jpg | |
| 2021-03-08 07:31 | gstecher | File Deleted: RAxML_MajorityRuleConsensusTree.withoutRogues | |
| 2021-03-12 09:35 | gstecher | Note Added: 0004562 | |
| 2021-03-12 09:35 | gstecher | Status | new => resolved |
| 2021-03-12 09:35 | gstecher | Resolution | open => won't fix |
| 2021-03-12 09:35 | gstecher | Assigned To | => gstecher |
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Issue History |
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