FitMultiModel#
HyPhy version required  ≥ 2.5.7 
Parallel support  MP 
File path  TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf 
Standard analysis menu  FMM 
Citation  Preprint 
What biological question is the method designed to answer?#
Does a data set have evidence of multiple simultaneous hits (MH) and to what exitent?
What are the recommended applications?#
FMM can be useful if a scientist wishes to see if MH exsist in their data and the potential impact of those MH. FMM will also provide a list of sites that show strong preference for codon models with multiple hits that may be used for further exploration.
What is the statistical procedure and statistical test is used to establish significance for this method?#
For each alignment the following models are fit to the data:

1H: The standard Muse and Gaut (1994) codon model that allows for only single instantaneous nucleotide changes

2H: an extension of the 1H model that allows two nucleotides in a codon to be substituted instantaneously with rate δ relative to 1H synonymous rate

3HSI: the 2H model extended to allow three simultaneous nucleotide substitutions in a codon if the change is synonymous with relative rate, ψ_{s}

3H: the 2H model extend to allow any three nucleotide simultanceous substitutions with relative rate ψ

3H+: the 3HSI model extended to permit any threenulceotide substitutions with relative rate ψ
See the following table for a breakdown of parameters and if they are estimated for each model:
Model  
Parameter  Description  1H  2H  3HSI  3H  3H+ 
ω_{i}  Site dN/dS ratio  Random effect 3bin GDD distribution  
δ  Global 2H/1H rate ratio  0  Estimated  Estimated  Estimated  Estimated 
ψ_{s}  Global 3H/1H rate ratio for synonymous codon islands  0  Estimated  Estimated  = ψ  Estimated 
ψ  Global 3H/1H rate ratio  0  0  0  Estimated  Estimated 
The actual statistical test being performed are pairwise likelihood ratio test between the models such that the null is always the model with fewer parameters eg: 1H v 2H, 1H  null and 2H alternative.
How should one interpret positive and negative test results?#
A positive result (ie p ≤ 0.05) for a likelihood ratio test between two models, H_{0} and H_{A}, means that we reject H_{0}. For example, if we look at a LRT between 1H and 2H, where 1H is H_{0} and 2H is H_{A}, a p value ≤ 0.05 means we can reject the hypothesis that 2H has zero rates.
A negative result (ie p > 0.05) means we fail to reject the null. Thus in the same example as above (1H vs 2H) we would fail to reject the hypothesis that 2H has zero rates.
Rules of thumb for when this method is likely to work well, and when it is not.#
This method is likely to work well on trees with longer branches and sequences. It is not likely to work well on shorter trees.
Example#
For more information about running options see here
HYPHYMP FitMultiModel.bf alignment p51.nex tripleislands Yes
The following data are output to the screen.
Analysis Description#
Examine whether or not a codon alignment is better fit by models which permit multiple instantaneous substitutions. v0.2 adds a separate rate for codonisland triplehit rates

Requirements: inframe codon alignment and a phylogenetic tree

Written by: Sergei L Kosakovsky Pond, Sadie Wisotsky and Alexander Lucaci

Contact Information: spond@temple.edu

Analysis Version: 0.2
code –> Universal Loaded a multiple sequence alignment with 8 sequences, 440 codons, and 1 partitions from
/home/swisotsky/hyphyanalyses/FitMultiModel/p51.nex
The number of omega rate classes to include in the model (permissible range = [1,10], default value = 3, integer): rates –> 3tripleislands –> Yes
Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model#
 Log(L) = 3320.50, AICc = 6683.09 (21 estimated parameters)
Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases#
 Log(L) = 3178.60, AICc = 6413.66 (28 estimated parameters)
 nonsynonymous/synonymous rate ratio for test = 0.2459
Fitting Standard MG94#
 Log(L) = 3121.04, AICc = 6308.73 (33 estimated parameters)
 nonsynonymous/synonymous rate ratio = 0.2967
 The following relative rate distribution (mean 1) for sitetosite nonsynonymous rate variation was inferred
Rate  Proportion, %  Notes 

0.186  86.040  
4.466  13.674  
80.143  0.286 
Fitting MG94 with double instantaneous substitutions#
 Log(L) = 3121.03, AICc = 6310.74 (34 estimated parameters)
 nonsynonymous/synonymous rate ratio = 0.2946
 rate at which 2 nucleotides are changed instantly within a single codon = 0.0127
 The following relative rate distribution (mean 1) for sitetosite nonsynonymous rate variation was inferred
Rate  Proportion, %  Notes 

0.186  85.954  
4.448  13.757  
79.054  0.289 
Fitting MG94 with double and triple instantaneous substitutions#
 Log(L) = 3121.03, AICc = 6314.82 (36 estimated parameters)
 nonsynonymous/synonymous rate ratio = 0.2947
 rate at which 2 nucleotides are changed instantly within a single codon = 0.0127
 rate at which 3 nucleotides are changed instantly within a single codon = 0.0000
 rate at which 3 nucleotides are changed instantly within a single codon between synonymous codon islands = 0.0000
 The following relative rate distribution (mean 1) for sitetosite nonsynonymous rate variation was inferred
Rate  Proportion, %  Notes 

0.186  85.952  
4.444  13.756  
78.643  0.291 
Fitting MG94 with double and triple instantaneous substitutions [only synonymous islands]#
 Log(L) = 3121.03, AICc = 6312.78 (35 estimated parameters)
 nonsynonymous/synonymous rate ratio = 0.2946
 rate at which 2 nucleotides are changed instantly within a single codon = 0.0126
 rate at which 3 nucleotides are changed instantly within a single codon = 0.0000
 rate at which 3 nucleotides are changed instantly within a single codon between synonymous codon islands = 0.0000
 The following relative rate distribution (mean 1) for sitetosite nonsynonymous rate variation was inferred
Rate  Proportion, %  Notes 

0.186  85.959  
4.451  13.751  
78.760  0.290 
Summary of rate estimates and significance testing#
Model  LogL  omega  2hit rate  pvalue  3hit rate  pvalue 

Standard MG94  3121.04  0.2967  N/A  N/A  N/A  N/A 
Standard MG94 + 2 hits  3121.03  0.2946  0.0127  0.8622 (2hit rate = 0)  N/A  N/A 
Standard MG94 + 3 hits (islands)  3121.03  0.2946  0.0000  0.9960 (3hit island vs 2hit)  0.0000  1.0000 (3hit = 0) 
Standard MG94 + 2 or 3 hits  3121.03  0.2947  0.0127  0.9986 (2&3hit rates = 0)  0.0000  1.0000 (3hit rate(s) = 0) 