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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0004043 | MEGA | File Conversion | public | 2022-10-31 12:02 | 2023-06-17 09:43 |
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| 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 | | |
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| Summary | 0004043: one specific alignment won't convert filetypes from fasta to phylip 3.0, but others do. |
| Description | Open protein sequence alignment file XHA_N50.mas
convert file to fasta format
open fasta file for analysis (protein sequences)
deselect option for conservation shown as dots
export data from fasta to phylip 3.0 interleaved |
| Steps To Reproduce | I have a MEGAX alignment of full length proteins within a protein family. I delete the first 50 amino acids and then save the file and make two additional copies by just ctrl-c/ctrl-v in the folder where I keep the file. I now have 3 files. One of the three remains unchanged. A second one has 10 new protein sequences added, then I delete the C-terminal (righthand) end of the protein. A third one does not have any new sequences added, and a larger portion of the N-terminal (lefthand) region is deleted. I am left with a file containing a full-length protein alignment with 52 proteins, a c-terminal protein alignment with 52 proteins, and an N terminal protein alignment with 62 proteins. I successfully convert all three alignments to fasta format, then open them one by one with MEGAX again and select "analyze" and "protein sequence" without changing any other settings when prompted to choose what I'd like to do with the file. I deselect the option that automatically shows positions of conservation as dots and I either click on one of the toolbar buttons for exporting data or I open the data dropdown menu and select "export data...". In the new interface that opens I select phylip 3.0 as my target format and leave all other settings unchanged (my desired file output is interleaved). The files containing full length and c terminus alignments export to phylip file type without issue. After the conversion is complete the program asks if I'd like to view the file. I select 'no' and close the open data file. for ONLY the N terminus alignment, the program crashes without any error messages and before the popup opens that asks if I'd like to view the file. It successfully creates a .phy document with the correct name, but the document is blank. I've tried remaking the file from the original .mas but this does not fix the problem. I have tried remaking the other files to see if the whole program was stuck, but the other files once again converted successfully. There are no visual problems with the N terminus alignment file. |
| Tags | No tags attached. |
| Attach Tags | (Separate by ",")
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| First Name | Katie |
| Last Name | Horton |
| Email | katie.n.horton@mail.missouri.edu |
| Confirm Email | katie.n.horton@mail.missouri.edu |
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| Attached Files |  XHA_N50.mas (11,710 bytes) 2022-10-31 12:02 |
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