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IDProjectCategoryView StatusDate SubmittedLast Update
0001251MEGACalculation Errorpublic2019-05-29 10:212023-04-14 00:58
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSLinux 
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
Summary0001251: zero probabilities while reconstructing ancestors
DescriptionHello,
I am trying to reconstruct ancestors for the simulated dataset (attached) using the tree built by Fasttree (attached). Several positions have zero probabilities for any of four nucleotides at internal nodes (e.g. 8 and 18) resulting in ancestral sequences shorter than the current ones. I am wondering how my dataset results in such behavior; I have never had such a problem before with real data.

Thank you.
Steps To ReproduceLaunch ancestor reconstruction with the following config file:

; Please do not edit this file! If this file is modified, results are unpredictable.
; Instead of modifying this file, simply create a new MEGA Analysis Options file by using the MEGA Prototyper.
[ MEGAinfo ]
ver = 7160929-x86_64 Linux
[ DataSettings ]
datatype = snNucleotide
containsCodingNuc = False
MissingBaseSymbol = ?
IdenticalBaseSymbol = .
GapSymbol = -
[ ProcessTypes ]
ppAncSeq = true
ppML = true
[ AnalysisSettings ]
Analysis = Ancestral Sequence Inference
Tree to Use = Use tree from file
Statistical Method = Maximum Likelihood
Substitution Model = ====================
Substitutions Type = Nucleotide
Model/Method = General Time Reversible model
Rates and Patterns = ====================
Rates among Sites = Gamma Distributed With Invariant Sites (G+I)
No of Discrete Gamma Categories = 4
Data Subset to Use = ====================
Gaps/Missing Data Treatment = Use all sites
Site Coverage Cutoff (%) = Not Applicable
Branch Swap Filter = None
Has Time Limit = False
Maximum Execution Time = -1
TagsNo tags attached.
Attach Tags (Separate by ",")
First NameKsenia
Last NameSafina
Emailk.r.safina@gmail.com
Confirm Emailk.r.safina@gmail.com
Attached Fileszip file icon to_reproduce.zip (4,092 bytes) 2019-05-29 10:21

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- Issue History
Date Modified Username Field Change
2019-05-29 10:21 guest New Issue
2019-05-29 10:21 guest File Added: to_reproduce.zip
2022-03-08 07:37 guest Note Added: 0005024
2022-12-05 07:03 guest Note Added: 0005913
2023-04-14 00:58 guest Note Added: 0006426

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