MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0002228MEGACalculation Errorpublic2020-09-12 06:372023-04-14 18:41
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSWindowsOS Version10
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameJeff
Last NameMower
Emailjpmower@unl.edu
Confirm Emailjpmower@unl.edu
Summary0002228: ML with GTR+G+I model produces incorrect tree
DescriptionI have a data set of 20 plastid gene sequences from gymnosperms plus some outgroups. The point of this data set is to assess the position of a difficult taxon (Gnetidae) among gymnosperms. Gnetidae are well-known as a problematic group in plant systematics.

I evaluated this data set using ML with a GTR+G+I model with RAxML, phyML, IQ-TREE and MEGA. MEGA failed to obtain the same tree as the other three programs. However, I do get the correct tree with MEGA using a GTR+G model.

It seems there may be a problem with your parameter optimization when rate heterogeneity is estimated using both a gamma distribution and a proportion of invariant sites. Or perhaps with your SPR tree searching algorithm.
Steps To ReproduceOpened data file: Gnetidae.fas. It is nucleotide, protein-coding, standard genetic code.

"Construct/Test Maximum Likelihood Tree” with the following choices:
Test of Phylogeny: None
Substitutions Type: Nucleotide
Model/Method: GTR
Rates among Sites: Gamma Distributed With Invariant Sites (G+I)
No of Discrete Gamma Categories: 5
Gaps/Missing Data Treatment: Use all sites
Select Codon Positions: selected all (1st, 2nd, 3rd, Noncoding)
ML Heuristic Method: Subtree-Pruning-Regrafting - Extensive (SPR level 5)
Initial Tree for ML: Make initial trees automatically (Default - NJ/BioNJ)
Branch Swap Filter: None
Number of Threads: 7
Additional InformationI've submitted a zip file with results from all four programs.
TagsNo tags attached.
Relationships
Attached Fileszip MLRuns.zip (908,572) 2020-09-12 06:37
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
2020-09-12 06:37guestNew Issue
2020-09-12 06:37guestFile Added: MLRuns.zip
2022-03-08 07:23guestNote Added: 0004962
2022-12-05 06:43guestNote Added: 0005810
2023-04-14 18:41guestNote Added: 0006528

Notes
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2023-04-14 18:41   
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