Whole Genome Phylogenies Using Sequence Environments

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Documentation for package ‘EnvNJ’ version 0.1.3

• DESCRIPTION file.
• Package NEWS.

Help Pages

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