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EnvNJ  

Whole Genome Phylogenies Using Sequence Environments
View on CRAN: Click here


Download and install EnvNJ package within the R console
Install from CRAN:
install.packages("EnvNJ")

Install from Github:
library("remotes")
install_github("cran/EnvNJ")

Install by package version:
library("remotes")
install_version("EnvNJ", "0.1.3")



Attach the package and use:
library("EnvNJ")
Maintained by
Juan Carlos Aledo
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-05-31
Latest Update: 2021-09-27
Description:
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) . 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.
How to cite:
Juan Carlos Aledo (2021). EnvNJ: Whole Genome Phylogenies Using Sequence Environments. R package version 0.1.3, https://cran.r-project.org/web/packages/EnvNJ. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.1.2 (2021-05-31 09:00)
Other packages that cited EnvNJ R package
View EnvNJ citation profile
Other R packages that EnvNJ depends, imports, suggests or enhances
Complete documentation for EnvNJ
Functions, R codes and Examples using the EnvNJ R package
Some associated functions: aa.at . aa.comp . aaf . bovids . cos2dis . d.phy2df . df2fasta . env.extract . env.fasta . env.matrices . env.sp . envfascpp . envnj . fastaconc . metrics . msa.merge . msa.tree . ncd . ncdnj . ngraMatrix . ngram . otu.space . otu.vector . reyes . svdgram . vcos . vdis . vect2tree . vtree . 
Some associated R codes: ancillary.R . bovids.R . dataprep.R . envcoding.R . envfas.R . envnj.R . metrics.R . msa.R . ncdnj.R . ngram.R . reyes.R .  Full EnvNJ package functions and examples
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