R: Whole Genome Phylogenies Using Sequence Environments

# Whole Genome Phylogenies Using Sequence Environments

## 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