MantisBT - MEGA |
| View Issue Details |
|
| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0001669 | MEGA | Calculation Error | public | 2019-12-25 13:53 | 2019-12-25 13:53 |
|
| Reporter | guest | |
| Assigned To | | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | new | Resolution | open | |
| Platform | PC | OS | Linux | OS Version | other |
| Product Version | | |
| Target Version | | Fixed in Version | | |
| First Name | Galya |
| Last Name | Klink |
| Email | galkaklink@gmail.com |
| Confirm Email | galkaklink@gmail.com |
|
| Summary | 0001669: uncorrect uncestral states reconstruction |
| Description | During the ancestral states reconstruction for amino acid sequences, in some sites all ancestral states were reconstructed as gaps, despite that only few or no gaps were in alignments of sequences on the tips of the tree. |
| Steps To Reproduce | |
| Additional Information | I attached files:
1) *.mao file that was created by MEGA on Windows
2) an amino acid alignment of extant sequences (prot.more400AA.fasta)
3) a phylogenetic tree (MetFung.Einsi.RightTopology.newick)
4) a file MEGA.strange_sites.COX1_part2.mtREV. This is a list of sites where all ancestral states were reconstructed as gaps, but it was less than 10% of tips with gap in them.
first column - gene (does not mean sense), second column - site number in alignment, third column - number of tree tips with gaps (among 4350 tips), last column - number of internal nodes with gaps (it is equal to number of internal nodes for these subset of sites). |
| Tags | No tags attached. |
| Relationships | |
| Attached Files |  DATA.rar (237,030) 2019-12-25 13:53
https://megasoftware.net/mantis_bt/ |
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| Issue History |
| Date Modified | Username | Field | Change |
| 1969-12-31 17:33 | user19 | Note Added: 0001465 | |
| 1969-12-31 17:33 | user19 | Status | new => assigned |
| 1969-12-31 17:33 | user19 | Assigned To | => agasky |
| 1969-12-31 17:33 | agasky | Note Added: 0001598 | |
| 1969-12-31 17:33 | agasky | Status | assigned => resolved |
| 1969-12-31 17:33 | agasky | Resolution | open => fixed |
| 2019-12-25 13:53 | guest | New Issue | |
| 2019-12-25 13:53 | guest | File Added: DATA.rar | |
| 2020-01-02 07:24 | gstecher | Note Deleted: 0001465 | |
| 2020-01-02 07:24 | gstecher | Note Deleted: 0001598 | |