MantisBT - MEGA
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.
; 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
to_reproduce.zip (4,092) 2019-05-29 10:21https://megasoftware.net/mantis_bt/