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  "Package": "EnvNJ",
  "Type": "Package",
  "Title": "Whole Genome Phylogenies Using Sequence Environments",
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  "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<doi:10.1093/bioinformatics/18.1.100>. 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.",
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  "Author": "Juan Carlos Aledo [aut, cre]\n(<https://orcid.org/0000-0002-3497-9945>)",
  "Maintainer": "Juan Carlos Aledo <caledo@uma.es>",
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        "Bubalus_bubalis",
        "Bubalus_depressicornis",
        "Bos_grunniens",
        "Bos_indicus",
        "Bos_javanicus",
        "Bos_primigenius",
        "Bison_bison",
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        "Syncerus_caffer"
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      "title": "13 orthologous mtDNA-encoded proteins of 34 mammalian species.",
      "object": "reyes",
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        "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"
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      "title": "Residue Found at the Requested Position",
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      "page": "aa.comp",
      "title": "Amino Acid Composition",
      "topics": [
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    {
      "page": "aaf",
      "title": "Compute the Frequency of Each Amino Acid in Each Species",
      "topics": [
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      ]
    },
    {
      "page": "bovids",
      "title": "13 orthologous mtDNA-encoded proteins of 11 bovine species.",
      "topics": [
        "bovids"
      ]
    },
    {
      "page": "cos2dis",
      "title": "Convert Cosines Between Vectors into Pairwise Dissimilarities",
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      ]
    },
    {
      "page": "d.phy2df",
      "title": "Convert a Phylip Distance Matrix into a DataFrame",
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      "topics": [
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      ]
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    {
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      ]
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      "title": "Pairwise Vector Dissimilarities",
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      "title": "Carry Out a MSA of a Set of Different Orthologous Proteins",
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      "title": "Infer a tree based on a MSA",
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      "page": "ncd",
      "title": "Compute Normalized Compression Distances",
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