{ "_id": "6a55e5e0ff0138dec5d6a4e4", "Package": "EnvNJ", "Type": "Package", "Title": "Whole Genome Phylogenies Using Sequence Environments", "Version": "0.1.3", "Authors@R": "person(given = \"Juan Carlos\",\nfamily = \"Aledo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"caledo@uma.es\",\ncomment = c(ORCID = \"0000-0002-3497-9945\"))", "Description": "Contains utilities for the analysis of protein sequences\nin a phylogenetic context. Allows the generation of\nphylogenetic trees base on protein sequences in an\nalignment-independent way. Two different methods have been\nimplemented. One approach is based on the frequency analysis of\nn-grams, previously described in Stuart et al. (2002)\n. The other approach is\nbased on the species-specific neighborhood preference around\namino acids. Features include the conversion of a protein set\ninto a vector reflecting these neighborhood preferences,\npairwise distances (dissimilarity) between these vectors, and\nthe generation of trees based on these distance matrices.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-14 07:25:19 UTC", "User": "root" }, "Author": "Juan Carlos Aledo [aut, cre]\n()", "Maintainer": "Juan Carlos Aledo ", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev zlib1g-dev", "Repository": "https://jcaledo.r-universe.dev", "Date/Publication": "2021-09-27 09:50:02 UTC", "RemoteUrl": "https://github.com/cran/EnvNJ", "RemoteRef": "HEAD", "RemoteSha": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "_user": "jcaledo", "_type": "src", "_file": "EnvNJ_0.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/eb7c3ef24c46e1e41462466d96a889b85c4346a7ead45a059a67cba44692fa71", "_filesize": 266358, "_sha256": "eb7c3ef24c46e1e41462466d96a889b85c4346a7ead45a059a67cba44692fa71", "_expires": "2026-10-22T07:31:42.000Z", "_created": "2026-07-14T07:25:19.000Z", "_published": "2026-07-14T07:31:44.143Z", "_jobs": [ { "job": 87025393733, "time": 271, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8303473140" }, { "job": 87025393780, "time": 264, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8303470638" }, { "job": 87025393746, "time": 198, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8303446556" }, { "job": 87025393842, "time": 154, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8303431630" }, { "job": 87024479360, "time": 314, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8303376466" }, { "job": 87025393720, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8303420128" }, { "job": 87025393782, "time": 290, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8303480504" }, { "job": 87025393765, "time": 334, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8303495110" }, { "job": 87025393791, "time": 284, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8303477498" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620", "_status": "success", "_upstream": "https://github.com/cran/EnvNJ", "_commit": { "id": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "author": "Juan Carlos Aledo ", "committer": "cran-robot ", "message": "version 0.1.3\n", "time": 1632736202 }, "_maintainer": { "name": "Juan Carlos Aledo", "email": "caledo@uma.es", "login": "jcaledo", "description": "", "uuid": 10573051, "orcid": "0000-0002-3497-9945" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "bio3d", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "philentropy", "role": "Imports" }, { "package": "seqinr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "jcaledo", "count": 2, "uuid": 10573051 } ], "_userbio": { "uuid": 10573051, "type": "user", "name": "Juan Carlos Aledo", "followers": 1 }, "_downloads": { "count": 251, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/EnvNJ" }, "_searchresults": 11, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EnvNJ.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "jcaledo", "_cranurl": false, "_releases": [ { "version": "0.1.2", "date": "2021-05-31" }, { "version": "0.1.3", "date": "2021-09-27" } ], "_exports": [ "aa.at", "aa.comp", "aaf", "cos2dis", "d.phy2df", "df2fasta", "env.extract", "env.fasta", "env.matrices", "env.sp", "envfascpp", "envnj", "fastaconc", "metrics", "msa.merge", "msa.tree", "ncd", "ncdnj", "ngram", "ngraMatrix", "otu.space", "otu.vector", "svdgram", "vcos", "vdis", "vect2tree", "vtree" ], "_datasets": [ { "name": "bovids", "title": "13 orthologous mtDNA-encoded proteins of 11 bovine species.", "object": "bovids", "class": [ "data.frame" ], "fields": [ "Bos_taurus", "Bubalus_bubalis", "Bubalus_depressicornis", "Bos_grunniens", "Bos_indicus", "Bos_javanicus", "Bos_primigenius", "Bison_bison", "Bison_bonasus", "Pseudoryx_nghetinhensis", "Syncerus_caffer" ], "rows": 13, "table": true, "tojson": true }, { "name": "reyes", "title": "13 orthologous mtDNA-encoded proteins of 34 mammalian species.", "object": "reyes", "class": [ "data.frame" ], "fields": [ "Homo_sapiens", "Pan_troglodytes", "Pan_paniscus", "Gorilla_gorilla", "Pongo_pygmaeus", "Hylobates_lar", "Papio_hamadryas", "Equus_caballus", "Equus_asinus", "Rhinoceros_unicornis", "Ceratotherium_simum", "Phoca_vitulina", "Halichoerus_grypus", "Felis_catus", "Canis_lupus", "Balaenoptera_physalus", "Balaenoptera_musculus", "Bos_taurus", "Ovis_aries", "Sus_scrofa", "Hippopotamus_amphibius", "Artibeus_jamaicensis", "Loxodonta_africana", "Orycteropus_afer", "Dasypus_novemcinctus", "Oryctolagus_cuniculus", "Cavia_porcellus", "Glis_glis", "Rattus_norvegicus", "Mus_musculus", "Sciurus_vulgaris", "Didelphis_virginiana", "Macropus_robustus", "Ornithorhynchus_anatinus" ], "rows": 13, "table": true, "tojson": true } ], "_help": [ { "page": "aa.at", "title": "Residue Found at the Requested Position", "topics": [ "aa.at" ] }, { "page": "aa.comp", "title": "Amino Acid Composition", "topics": [ "aa.comp" ] }, { "page": "aaf", "title": "Compute the Frequency of Each Amino Acid in Each Species", "topics": [ "aaf" ] }, { "page": "bovids", "title": "13 orthologous mtDNA-encoded proteins of 11 bovine species.", "topics": [ "bovids" ] }, { "page": "cos2dis", "title": "Convert Cosines Between Vectors into Pairwise Dissimilarities", "topics": [ "cos2dis" ] }, { "page": "d.phy2df", "title": "Convert a Phylip Distance Matrix into a DataFrame", "topics": [ "d.phy2df" ] }, { "page": "df2fasta", "title": "Convert Dataframe into Fasta File", "topics": [ "df2fasta" ] }, { "page": "env.extract", "title": "Sequence Environment Around a Given Position", "topics": [ "env.extract" ] }, { "page": "env.fasta", "title": "Build Trees Based on the Environment Around the Indicated Amino Acid(s)", "topics": [ "env.fasta" ] }, { "page": "env.matrices", "title": "Environment Matrices", "topics": [ "env.matrices" ] }, { "page": "env.sp", "title": "Extract the Sequence Environments", "topics": [ "env.sp" ] }, { "page": "envfascpp", "title": "Convert Fasta Files into Environment Vectors", "topics": [ "envfascpp" ] }, { "page": "envnj", "title": "Build Trees Based on the Environment Around the Indicated Amino Acid(s)", "topics": [ "envnj" ] }, { "page": "fastaconc", "title": "Concatenate Fasta Files in a Single Multispecies Fasta File", "topics": [ "fastaconc" ] }, { "page": "metrics", "title": "Pairwise Vector Dissimilarities", "topics": [ "metrics" ] }, { "page": "msa.merge", "title": "Carry Out a MSA of a Set of Different Orthologous Proteins", "topics": [ "msa.merge" ] }, { "page": "msa.tree", "title": "Infer a tree based on a MSA", "topics": [ "msa.tree" ] }, { "page": "ncd", "title": "Compute Normalized Compression Distances", "topics": [ "ncd" ] }, { "page": "ncdnj", "title": "Compute a Distance Matrix Using Normalized Compression Distance", "topics": [ "ncdnj" ] }, { "page": "ngram", "title": "Compute n-Gram Frequencies Vector", "topics": [ "ngram" ] }, { "page": "ngraMatrix", "title": "Compute n-Gram Frequencies Dataframe", "topics": [ "ngraMatrix" ] }, { "page": "otu.space", "title": "Compute the Matrix Representing the Species Vector Subspace", "topics": [ "otu.space" ] }, { "page": "otu.vector", "title": "Convert a Set of Sequence Environments into a Vector", "topics": [ "otu.vector" ] }, { "page": "reyes", "title": "13 orthologous mtDNA-encoded proteins of 34 mammalian species.", "topics": [ "reyes" ] }, { "page": "svdgram", "title": "Compute Phylogenetic Trees Using an n-Gram and SVD Approach", "topics": [ "svdgram" ] }, { "page": "vcos", "title": "Compute Pairwise Cosines of the Angles Between Vectors", "topics": [ "vcos" ] }, { "page": "vdis", "title": "Compute Pairwise Distances Between Vectors", "topics": [ "vdis" ] }, { "page": "vect2tree", "title": "Convert a Set of Vectors into a Tree", "topics": [ "vect2tree" ] }, { "page": "vtree", "title": "Build a Tree When Species Are Encoded by n-Dim Vectors", "topics": [ "vtree" ] } ], "_rundeps": [ "ade4", "ape", "bio3d", "cli", "cpp11", "digest", "fastmatch", "generics", "glue", "igraph", "KernSmooth", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "nlme", "phangorn", "philentropy", "pixmap", "pkgconfig", "poorman", "quadprog", "Rcpp", "RcppArmadillo", "RcppParallel", "rlang", "segmented", "seqinr", "sp", "stringi", "stringr", "vctrs" ], "_score": 1.0413926851582251, "_indexed": true, "_nocasepkg": "envnj", "_universes": [ "jcaledo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.3", "date": "2026-07-14T07:27:36.000Z", "distro": "resolute", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/51c3ee5d6c2e8a068a4e7e2dd7d239e1dd09ed199c1df6cf7cdd4160670fe6e9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.6.1", "os": "linux", "version": "0.1.3", "date": "2026-07-14T07:27:33.000Z", "distro": "resolute", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/9a05a43233e5d2342c339159f71426450bae1bdcc95f26395a78c72bce9ee791", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.5.3", "os": "mac", "version": "0.1.3", "date": "2026-07-14T07:27:10.000Z", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/9d1b528be7491fe48bc9f700c12da9ec5c43b821aa98d85cc587ff72217ab60a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.6.1", "os": "mac", "version": "0.1.3", "date": "2026-07-14T07:26:46.000Z", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/eaff790e74bf7a73146c22e52462d4bb1d76c44eab5d2c667afd90032795d386", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.3", "date": "2026-07-14T07:27:43.000Z", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/745cb0f0cf56a732de9e2bf92e8e319e6fe19af3a070a21da496dc5fb0b85d6d", "status": "success", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.7.0", "os": "win", "version": "0.1.3", "date": "2026-07-14T07:26:53.000Z", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/1a648ee69bc3a74527611b41d42e6393858acf5d7dc331010df4465eed076024", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.5.3", "os": "win", "version": "0.1.3", "date": "2026-07-14T07:26:46.000Z", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/acb5310df7336aa394c8439403e590bbc437523ffc4ace118591938b309bf66a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" }, { "r": "4.6.1", "os": "win", "version": "0.1.3", "date": "2026-07-14T07:26:40.000Z", "commit": "e5e6a81a21b56cd9eabe67f964b1cea227303b8d", "fileid": "https://r2.ropensci.org/be8ee74cc8089c476bd76ea669507fdce7ce55f66afba11c8de5da67a25ded4b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jcaledo/actions/runs/29314209620" } ] }