Whole Genome Phylogenies Using Sequence Environments

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Documentation for package ‘EnvNJ’ version 0.1.3

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aa.at Residue Found at the Requested Position
aa.comp Amino Acid Composition
aaf Compute the Frequency of Each Amino Acid in Each Species
bovids 13 orthologous mtDNA-encoded proteins of 11 bovine species.
cos2dis Convert Cosines Between Vectors into Pairwise Dissimilarities
d.phy2df Convert a Phylip Distance Matrix into a DataFrame
df2fasta Convert Dataframe into Fasta File
env.extract Sequence Environment Around a Given Position
env.fasta Build Trees Based on the Environment Around the Indicated Amino Acid(s)
env.matrices Environment Matrices
env.sp Extract the Sequence Environments
envfascpp Convert Fasta Files into Environment Vectors
envnj Build Trees Based on the Environment Around the Indicated Amino Acid(s)
fastaconc Concatenate Fasta Files in a Single Multispecies Fasta File
metrics Pairwise Vector Dissimilarities
msa.merge Carry Out a MSA of a Set of Different Orthologous Proteins
msa.tree Infer a tree based on a MSA
ncd Compute Normalized Compression Distances
ncdnj Compute a Distance Matrix Using Normalized Compression Distance
ngram Compute n-Gram Frequencies Vector
ngraMatrix Compute n-Gram Frequencies Dataframe
otu.space Compute the Matrix Representing the Species Vector Subspace
otu.vector Convert a Set of Sequence Environments into a Vector
reyes 13 orthologous mtDNA-encoded proteins of 34 mammalian species.
svdgram Compute Phylogenetic Trees Using an n-Gram and SVD Approach
vcos Compute Pairwise Cosines of the Angles Between Vectors
vdis Compute Pairwise Distances Between Vectors
vect2tree Convert a Set of Vectors into a Tree
vtree Build a Tree When Species Are Encoded by n-Dim Vectors