Quantify the Extent of Evolutionary Evidence in Molecular Sequences

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Documentation for package ‘queeems’ version 1.0.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

queeems-package	Quantify the Extent of Evolutionary Evidence in Molecular Sequences
aboutQueeems	References Relevant to the 'queeems' Package
basecensus	Protein Base Composition Numerics
basecensus-method	Protein Base Composition Numerics
baseFrequency	Counts Indicating Protein Base Prevalence
baseSummary	Protein Base Composition Numerics
baseSummary-class	Protein Base Composition Numerics
BFs	Substitution Saturation Output: Bayesian Paradigm
BFs-method	Substitution Saturation Output: Bayesian Paradigm
BFthreshold	Substitution Saturation Output: Bayesian Paradigm
BFthreshold-method	Substitution Saturation Output: Bayesian Paradigm
bstringCodons	Convert a BStringSet Object to Codon Sequences
bstringCodons-method	Convert a BStringSet Object to Codon Sequences
bstringCodons.BStringSet	Convert a BStringSet Object to Codon Sequences
citing	Useful Package Citations
citing-class	Useful Package Citations
CnCs	Synonymous and Non-Synonymous Codon Match Counts
cncsentropy	Global [Non-]Synonymous Entropy Index for Protein Sequence
cncsframe	Synonymous and Non-Synonymous Frequencies
cncsframe-class	Synonymous and Non-Synonymous Frequencies
codondifferindex	Molecular Entropy Estimated from Codon Mismatches
codonDissimilarity	Codon Census Matrix Matched by Nucleotide Dissimilarity
codonDissimilarity-method	Codon Census Matrix Matched by Nucleotide Dissimilarity
codonDissimilarity.BStringSet	Codon Census Matrix Matched by Nucleotide Dissimilarity
datatype	Protein Base Composition Numerics
datatype-method	Protein Base Composition Numerics
diffNucBinary	Compare Codon Pairs to Identify Nucleotide Mismatch
entropyindex	Obtain Entropy Indices
fubarweights	FUBAR-like Weights
geneindex	Protein Information Entropy Handling
geneindex-class	Protein Information Entropy Handling
gentropy	Protein Information Entropy Handling
gentropy-method	Protein Information Entropy Handling
II.fasta	Paths to Example Protein Sequence Files
informula	Protein Information Entropy Handling
informula-method	Protein Information Entropy Handling
informula-method	Molecular Information Entropy Processor
LogL0	Substitution Saturation Output: Bayesian Paradigm
LogL0-method	Substitution Saturation Output: Bayesian Paradigm
LogL1	Substitution Saturation Output: Bayesian Paradigm
LogL1-method	Substitution Saturation Output: Bayesian Paradigm
mainPi	Substitution Saturation Output: Bayesian Paradigm
mainPi-method	Substitution Saturation Output: Bayesian Paradigm
mnomLogl	Approximate Log-Likelihood of a Multinomial Variable
molentropy	Molecular Entropy Generated Independently per Base Site
n2cFreqs	Generate Codon Frequencies from Nucleotide Frequencies
nonSynonymous	Identify Synonymous and Non-Synonymous Codons
nonvaries	Synonymous and Non-Synonymous Frequencies
nonvaries-method	Synonymous and Non-Synonymous Frequencies
nonvaries-method	Protein Information Entropy Handling
nonvaries-method	Substitution Saturation Output: Bayesian Paradigm
nonvaries-method	Molecular Information Entropy Processor
nORs	Synonymous and Non-Synonymous Frequencies
nORs-method	Synonymous and Non-Synonymous Frequencies
nseqs	Protein Base Composition Numerics
nseqs-method	Protein Base Composition Numerics
nsfreqs	Synonymous and Non-Synonymous Frequencies
nsfreqs-method	Synonymous and Non-Synonymous Frequencies
nucbalance	Synonymous and Non-Synonymous Frequencies
nucbalance-method	Synonymous and Non-Synonymous Frequencies
PI.fasta	Paths to Example Protein Sequence Files
queeems	Quantify the Extent of Evolutionary Evidence in Molecular Sequences
queeemsExtdata	Paths to Example Protein Sequence Files
renyiA	Protein Information Entropy Handling
renyiA-method	Protein Information Entropy Handling
renyiA-method	Molecular Information Entropy Processor
RTI.fasta	Paths to Example Protein Sequence Files
saturateBF	Substitution Saturation Output: Bayesian Paradigm
saturateBF-class	Substitution Saturation Output: Bayesian Paradigm
seqfilter	Delete Subset of Molecular Sequences
seqSaturation	Estimate Saturation Index For Protein Data
show-method	Protein Base Composition Numerics
show-method	Useful Package Citations
show-method	Synonymous and Non-Synonymous Frequencies
show-method	Protein Information Entropy Handling
show-method	Substitution Saturation Output: Bayesian Paradigm
show-method	Molecular Information Entropy Processor
si.renyi	Obtain Entropy Indices
si.shannon	Obtain Entropy Indices
sitecount	Protein Information Entropy Handling
sitecount-method	Protein Information Entropy Handling
sitecount-method	Substitution Saturation Output: Bayesian Paradigm
siteindices	Molecular Information Entropy Processor
siteindices-class	Molecular Information Entropy Processor
sitentropies	Molecular Information Entropy Processor
sitentropies-method	Molecular Information Entropy Processor
softmax	Softmax Transformation
summary-method	Substitution Saturation Output: Bayesian Paradigm
summary-method	Molecular Information Entropy Processor
useSyn	Protein Information Entropy Handling
useSyn-method	Protein Information Entropy Handling
VertCOI.fasta	Paths to Example Protein Sequence Files
wildtriplets	Synonymous and Non-Synonymous Frequencies
wildtriplets-method	Synonymous and Non-Synonymous Frequencies