Package: EnvNJ 0.1.3

EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.

Authors:Juan Carlos Aledo [aut, cre]

EnvNJ_0.1.3.tar.gz
EnvNJ_0.1.3.zip(r-4.5)EnvNJ_0.1.3.zip(r-4.4)EnvNJ_0.1.3.zip(r-4.3)
EnvNJ_0.1.3.tgz(r-4.4-any)EnvNJ_0.1.3.tgz(r-4.3-any)
EnvNJ_0.1.3.tar.gz(r-4.5-noble)EnvNJ_0.1.3.tar.gz(r-4.4-noble)
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EnvNJ.pdf |EnvNJ.html✨
EnvNJ/json (API)
NEWS

# Install 'EnvNJ' in R:
install.packages('EnvNJ', repos = c('https://jcaledo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • bovids - 13 orthologous mtDNA-encoded proteins of 11 bovine species.
  • reyes - 13 orthologous mtDNA-encoded proteins of 34 mammalian species.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.04 score 11 scripts 174 downloads 27 exports 32 dependencies

Last updated 3 years agofrom:e5e6a81a21. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winNOTENov 05 2024
R-4.5-linuxNOTENov 05 2024
R-4.4-winNOTENov 05 2024
R-4.4-macNOTENov 05 2024
R-4.3-winOKNov 05 2024
R-4.3-macOKNov 05 2024

Exports:aa.ataa.compaafcos2disd.phy2dfdf2fastaenv.extractenv.fastaenv.matricesenv.spenvfascppenvnjfastaconcmetricsmsa.mergemsa.treencdncdnjngramngraMatrixotu.spaceotu.vectorsvdgramvcosvdisvect2treevtree

Dependencies:ade4apebio3dclicpp11digestfastmatchgenericsglueigraphKernSmoothlatticelifecyclemagrittrMASSMatrixnlmephangornphilentropypixmappkgconfigpoormanquadprogRcppRcppArmadillorlangsegmentedseqinrspstringistringrvctrs

Readme and manuals

Help Manual

Help pageTopics
Residue Found at the Requested Positionaa.at
Amino Acid Compositionaa.comp
Compute the Frequency of Each Amino Acid in Each Speciesaaf
13 orthologous mtDNA-encoded proteins of 11 bovine species.bovids
Convert Cosines Between Vectors into Pairwise Dissimilaritiescos2dis
Convert a Phylip Distance Matrix into a DataFramed.phy2df
Convert Dataframe into Fasta Filedf2fasta
Sequence Environment Around a Given Positionenv.extract
Build Trees Based on the Environment Around the Indicated Amino Acid(s)env.fasta
Environment Matricesenv.matrices
Extract the Sequence Environmentsenv.sp
Convert Fasta Files into Environment Vectorsenvfascpp
Build Trees Based on the Environment Around the Indicated Amino Acid(s)envnj
Concatenate Fasta Files in a Single Multispecies Fasta Filefastaconc
Pairwise Vector Dissimilaritiesmetrics
Carry Out a MSA of a Set of Different Orthologous Proteinsmsa.merge
Infer a tree based on a MSAmsa.tree
Compute Normalized Compression Distancesncd
Compute a Distance Matrix Using Normalized Compression Distancencdnj
Compute n-Gram Frequencies Vectorngram
Compute n-Gram Frequencies DataframengraMatrix
Compute the Matrix Representing the Species Vector Subspaceotu.space
Convert a Set of Sequence Environments into a Vectorotu.vector
13 orthologous mtDNA-encoded proteins of 34 mammalian species.reyes
Compute Phylogenetic Trees Using an n-Gram and SVD Approachsvdgram
Compute Pairwise Cosines of the Angles Between Vectorsvcos
Compute Pairwise Distances Between Vectorsvdis
Convert a Set of Vectors into a Treevect2tree
Build a Tree When Species Are Encoded by n-Dim Vectorsvtree