Man pages for EnvNJ
Whole Genome Phylogenies Using Sequence Environments
| 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 |
| df2fasta | Convert Dataframe into Fasta File |
| d.phy2df | Convert a Phylip Distance Matrix into a DataFrame |
| env.extract | Sequence Environment Around a Given Position |
| envfascpp | Convert Fasta Files into Environment Vectors |
| env.fasta | Build Trees Based on the Environment Around the Indicated... |
| env.matrices | Environment Matrices |
| envnj | Build Trees Based on the Environment Around the Indicated... |
| env.sp | Extract the Sequence Environments |
| 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... |
| 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... |
| 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 |
