MantisBT
My View | View Issues | Report Issue | Change Log | Roadmap | My Account
  

View Issue Details [ Jump to Notes ] [ Issue History ] [ Print ]
IDProjectCategoryView StatusDate SubmittedLast Update
0002228MEGACalculation Errorpublic2020-09-12 06:372023-04-14 18:41
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSWindows 
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
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.
Attach Tags (Separate by ",")
First NameJeff
Last NameMower
Emailjpmower@unl.edu
Confirm Emailjpmower@unl.edu
Attached Fileszip file icon MLRuns.zip (908,572 bytes) 2020-09-12 06:37

- Relationships

- Upload Files
Select Files
(Maximum size: 5,000k)




-  Notes
(0004962)
guest (reporter)
2022-03-08 07:23

 https://www.bestwatchaaa.com/Hublot-replica.html [^] https://www.bestwatchaaa.com/Graham-replica.html [^] https://www.bestwatchaaa.com/Ebel-replica.html [^] https://www.bestwatchss.com/Breguet-Replica-Watches.html [^] became well-known after the introduction of its prominent Pilot s Watch https://www.bestwatchss.com/Nomos-Replica-Watches.html [^] was immediately appreciated https://www.goodswisswatch.com/ [^] aviators. Famous IWC watches are known for https://www.bestwatchaaa.com/Technomarine-replica.html [^] premium engineering and the brand https://www.bestwatchss.com/Zenith-Replica-Watches.html [^] https://www.bestwatchaaa.com/Longines-replica.html [^] become a https://www.bestwatchaaa.com/Girard-Perregaux-replica.html [^] of high-end watch-making. It https://www.bestwatchss.com/Jaeger-LeCoultre-Replica-Watches.html [^] known to everyone that how much https://www.bestwatchss.com/ [^] https://www.bestwatchaaa.com/Bedat-Co-replica.html [^] https://www.bestwatchss.com/Longines-Replica-Watches.html [^] https://www.fakeswatchs.com/ [^] Using https://www.copywatchstyle.com/ [^] replica https://www.bestwatchaaa.com/Bulgari-replica.html [^] are https://www.bestwatchss.com/A-Lange-Sohne-Replica-Watches.html [^] popular day https://www.hotwatchsreplica.com/ [^] day. People buy https://www.bestwatchaaa.com/Breitling-replica.html [^] IWC watches because https://www.bestwatchss.com/Glashutte-Replica-Watches.html [^] https://www.bestwatchaaa.com/TW-Steel-replica.html [^] available at amazingly https://www.bestwatchss.com/Panerai-Replica-Watches.html [^] prices. Replica https://www.bestwatchaaa.com/U-Boat-replica.html [^] https://www.bestwatchaaa.com/Tissot-replica.html [^] https://www.bestwatchss.com/Girard-Perregaux-Replica-Watches.html [^] in https://www.allswisswatchs.com/ [^] designs and https://www.bestwatchss.com/Oris-Replica-Watches.html [^] patterns and all the designs of https://www.bestwatchaaa.com/Breguet-replica.html [^] https://www.swissrepicass.com/ [^] replica https://www.allshopwatch.com/ [^] look absolutely https://www.bestwatchaaa.com/TAG-Heuer-replica.html [^] These https://www.bestwatchaaa.com/Chopard-replica.html [^] will https://www.bestwatchaaa.com/Piaget-replica.html [^] https://www.bestwatchss.com/Montblanc-Replica-Watches.html [^] your dream https://www.bestwatchss.com/Franck-Muller-Replica-Watches.html [^] true.
(0005810)
guest (reporter)
2022-12-05 06:43

 pinjaman dana jaminan bpkb mobil cepat hanya 1 hari bisa langsung cair dengan suku bunga rendah serta tanpa survey dan bpkb mobil aman untuk seluruh wilayah indonesia.

https://www.justgiving.com/fundraising/mandiripinjamandana [^]
https://ameblo.jp/mandiripinjamandana/entry-12680765607.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680767540.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680769727.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680770493.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680771364.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680785558.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680786359.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680787122.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680787855.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680788647.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680789550.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680790188.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680790735.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680791419.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680792163.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680792608.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680793459.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680793916.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680794272.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680794619.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680794959.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680795284.html [^]
https://ameblo.jp/mandiripinjamandana/entry-12680795637.html [^]
(0006528)
guest (reporter)
2023-04-14 18:41

 https://www.estoolcarbide.com/product/cemented-carbide-blades-lathe-cutting-for-steel-cnc-triangular-turning-tool-inserts/ [^] [TNMG Steel Inserts] https://harrisonbb.exblog.jp/ [^] [parting tool inserts] http://onlooker.livedoor.biz/ [^] [http://onlooker.livedoor.biz/ [^]] http://laborers.blog.jp/ [^] [http://laborers.blog.jp/ [^]] https://sidneysean.exblog.jp/ [^] [grooving inserts manufacturers] http://all-best.ldblog.jp/ [^] [http://all-best.ldblog.jp/ [^]] https://douglasvio.exblog.jp/ [^] [carbide wear rods] http://easytouse.blog.jp/ [^] [http://easytouse.blog.jp/ [^]] https://brenteden.exblog.jp/ [^] [indexable drill bit]

- Issue History
Date Modified Username Field Change
2020-09-12 06:37 guest New Issue
2020-09-12 06:37 guest File Added: MLRuns.zip
2022-03-08 07:23 guest Note Added: 0004962
2022-12-05 06:43 guest Note Added: 0005810
2023-04-14 18:41 guest Note Added: 0006528

Copyright © 2000 - 2024 MantisBT Team
Powered by Mantis Bugtracker