{
  "_id": "6a1b09551d7bb097a0a057eb",
  "Package": "syntenet",
  "Title": "Inference And Analysis Of Synteny Networks",
  "Version": "1.14.0",
  "Date": "2022-03-28",
  "Authors@R": "c(\nperson(given = \"Fabrício\",\nfamily = \"Almeida-Silva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fabricio_almeidasilva@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-5314-2964\")),\nperson(given = \"Tao\",\nfamily = \"Zhao\",\nrole = \"aut\",\nemail = \"tao.zhao@nwafu.edu.cn\",\ncomment = c(ORCID = \"0000-0001-7302-6445\")),\nperson(given = \"Kristian K\",\nfamily = \"Ullrich\",\nrole = \"aut\",\nemail = \"ullrich@evolbio.mpg.de\",\ncomment = c(ORCID = \"0000-0003-4308-9626\")),\nperson(given = \"Yves\",\nfamily = \"Van de Peer\",\nrole = \"aut\",\nemail = \"yves.vandepeer@psb.vib-ugent.be\",\ncomment = c(ORCID = \"0000-0003-4327-3730\"))\n)",
  "Description": "syntenet can be used to infer synteny networks from\nwhole-genome protein sequences and analyze them. Anchor pairs\nare detected with the MCScanX algorithm, which was ported to\nthis package with the Rcpp framework for R and C++ integration.\nAnchor pairs from synteny analyses are treated as an undirected\nunweighted graph (i.e., a synteny network), and users can\nperform: i. network clustering; ii. phylogenomic profiling (by\nidentifying which species contain which clusters) and; iii.\nmicrosynteny-based phylogeny reconstruction with maximum\nlikelihood.",
  "License": "GPL-3",
  "URL": "https://github.com/almeidasilvaf/syntenet",
  "BugReports": "https://support.bioconductor.org/t/syntenet",
  "biocViews": "Software, NetworkInference, FunctionalGenomics,\nComparativeGenomics, Phylogenetics, SystemsBiology,\nGraphAndNetwork, WholeGenome, Network",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:32 UTC",
  "RemoteUrl": "https://github.com/bioc/syntenet",
  "RemoteRef": "RELEASE_3_23",
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  "Packaged": {
    "Date": "2026-05-30 10:59:51 UTC",
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  "Author": "Fabrício Almeida-Silva [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5314-2964>),\nTao Zhao [aut] (ORCID: <https://orcid.org/0000-0001-7302-6445>),\nKristian K Ullrich [aut] (ORCID:\n<https://orcid.org/0000-0003-4308-9626>),\nYves Van de Peer [aut] (ORCID: <https://orcid.org/0000-0003-4327-3730>)",
  "Maintainer": "Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com>",
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      "page": "angiosperm_phylogeny",
      "title": "Microsynteny-based angiosperm phylogeny.",
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    },
    {
      "page": "annotation",
      "title": "Filtered genome annotation for Ostreococcus sp. species",
      "topics": [
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      "title": "List of data frames containing BLAST-like tabular output",
      "topics": [
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    },
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      "title": "Check if input objects are ready for further analyses",
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    },
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      "title": "Cluster the synteny network using the Infomap algorithm",
      "topics": [
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      "title": "Synteny network clusters of BUSCO genes for 25 eudicot species",
      "topics": [
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      "title": "Collapse a list of bidirectional DIAMOND hits",
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    },
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      "title": "Create a data frame of species IDs (3-5-character abbreviations)",
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      "title": "Check if DIAMOND is installed",
      "topics": [
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    },
    {
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      "title": "Synteny network of Ostreococcus genomes represented as an edge list",
      "topics": [
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    },
    {
      "page": "export_sequences",
      "title": "Export processed sequences as FASTA files",
      "topics": [
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    },
    {
      "page": "fasta2AAStringSetlist",
      "title": "Read FASTA files in a directory as a list of AAStringSet objects",
      "topics": [
        "fasta2AAStringSetlist"
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    },
    {
      "page": "find_GS_clusters",
      "title": "Find group-specific clusters based on user-defined species classification",
      "topics": [
        "find_GS_clusters"
      ]
    },
    {
      "page": "gff2GRangesList",
      "title": "Read GFF/GTF files in a directory as a GRangesList object",
      "topics": [
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    },
    {
      "page": "infer_microsynteny_phylogeny",
      "title": "Infer microsynteny-based phylogeny with IQTREE",
      "topics": [
        "infer_microsynteny_phylogeny"
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    },
    {
      "page": "infer_syntenet",
      "title": "Infer synteny network",
      "topics": [
        "infer_syntenet"
      ]
    },
    {
      "page": "interspecies_synteny",
      "title": "Detect interspecies synteny",
      "topics": [
        "interspecies_synteny"
      ]
    },
    {
      "page": "intraspecies_synteny",
      "title": "Detect intraspecies synteny",
      "topics": [
        "intraspecies_synteny"
      ]
    },
    {
      "page": "iqtree_is_installed",
      "title": "Check if IQTREE is installed",
      "topics": [
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      ]
    },
    {
      "page": "iqtree_version",
      "title": "Get IQ-TREE version",
      "topics": [
        "iqtree_version"
      ]
    },
    {
      "page": "last_is_installed",
      "title": "Check if last is installed",
      "topics": [
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      ]
    },
    {
      "page": "make_bidirectional",
      "title": "Create a data frame of bidirectional comparisons from unidirectional comparisons",
      "topics": [
        "make_bidirectional"
      ]
    },
    {
      "page": "network",
      "title": "Synteny network of BUSCO genes for 25 eudicot species",
      "topics": [
        "network"
      ]
    },
    {
      "page": "parse_collinearity",
      "title": "Parse .collinearity files obtained with MCScan",
      "topics": [
        "parse_collinearity"
      ]
    },
    {
      "page": "phylogenomic_profile",
      "title": "Perform phylogenomic profiling for synteny network clusters",
      "topics": [
        "phylogenomic_profile"
      ]
    },
    {
      "page": "plot_network",
      "title": "Plot network",
      "topics": [
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      ]
    },
    {
      "page": "plot_profiles",
      "title": "Plot a heatmap of phylogenomic profiles",
      "topics": [
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    },
    {
      "page": "process_input",
      "title": "Process sequence data",
      "topics": [
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    {
      "page": "profiles2phylip",
      "title": "Save the transposed binary profiles matrix to a file in PHYLIP format",
      "topics": [
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    },
    {
      "page": "proteomes",
      "title": "Filtered proteomes of Ostreococcus sp. species",
      "topics": [
        "proteomes"
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    },
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      "page": "rcpp_mcscanx_file",
      "title": "rcpp_mcscanx_file",
      "topics": [
        "rcpp_mcscanx_file"
      ]
    },
    {
      "page": "read_diamond",
      "title": "Read DIAMOND/BLAST tables as a list of data frames",
      "topics": [
        "read_diamond"
      ]
    },
    {
      "page": "run_diamond",
      "title": "Wrapper to run DIAMOND from an R session",
      "topics": [
        "run_diamond"
      ]
    },
    {
      "page": "run_last",
      "title": "Wrapper to run last from an R session",
      "topics": [
        "run_last"
      ]
    },
    {
      "page": "scerevisiae_annot",
      "title": "Genome annotation of the yeast species S. cerevisiae",
      "topics": [
        "scerevisiae_annot"
      ]
    },
    {
      "page": "scerevisiae_diamond",
      "title": "Intraspecies DIAMOND output for S. cerevisiae",
      "topics": [
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      ]
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