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  "Package": "ips",
  "Version": "0.1.0",
  "Date": "2025-09-15",
  "Title": "Interfaces to Phylogenetic Software in R",
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  "URL": "https://github.com/heibl/ips",
  "Description": "Functions that wrap popular phylogenetic software for\nsequence alignment, masking of sequence alignments, and\nestimation of phylogenies and ancestral character states.",
  "License": "GPL-3",
  "Language": "en-US",
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  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libglpk-dev make libxml2-dev",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2026-03-24 11:09:43 UTC",
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  "Author": "Christoph Heibl [aut, cre],\nNatalie Cusimano [aut],\nFranz-Sebastian Krah [aut],\nMartin R. Smith [ctb] (ORCID: <https://orcid.org/0000-0001-5660-1727>)",
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      "date": "2026-02-23"
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    "are.tips.consecutive",
    "assembleDataNode",
    "assembleDistributionNode",
    "assembleInitNode",
    "assembleLoggers",
    "assembleStateNode",
    "assembleTreeNode",
    "beastLog",
    "blastn",
    "code.simple.gaps",
    "collapseUnsupportedEdges",
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    "del.miss",
    "deleteEmptyCells",
    "deleteGaps",
    "descendants",
    "DNAbin2index",
    "eoi",
    "fixNodes",
    "forceEqualTipHeights",
    "gblocks",
    "identifyEmptyCells",
    "index2DNAbin",
    "mafft",
    "mafft.merge",
    "mrbayes",
    "mrbayes.lset",
    "mrbayes.mcmc",
    "mrbayes.prset",
    "multistateMCMC",
    "multistateML",
    "neighboringPairs",
    "noi",
    "ntip",
    "operator",
    "parameter",
    "partitionfinder",
    "pathd8",
    "phylo2mafft",
    "phylo2mst",
    "pis",
    "prank",
    "raxml",
    "raxml.partitions",
    "rbeauti",
    "rc",
    "read.beast",
    "read.beast.table",
    "read.fas",
    "read.mrbayes",
    "read.nex",
    "read.phy",
    "read.starbeast",
    "read.xml",
    "setClock",
    "sister",
    "splitIntoClades",
    "terminal.clades",
    "terminalSisters",
    "tipHeights",
    "traitRate",
    "trimEnds",
    "unlistFirstLevel",
    "unresolve.clade",
    "write.fas",
    "write.nex",
    "write.phy"
  ],
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      "title": "Bark Beetle 16S Sequences",
      "object": "ips.16S",
      "file": "ips.16S.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 42,
      "table": false,
      "tojson": false
    },
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      "name": "ips.28S",
      "title": "Bark Beetle 28S Sequences",
      "object": "ips.28S",
      "file": "ips.28S.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 28,
      "table": false,
      "tojson": false
    },
    {
      "name": "ips.cox1",
      "title": "Bark Beetle COX1 Sequences",
      "object": "ips.cox1",
      "file": "ips.cox1.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 26,
      "table": false,
      "tojson": false
    },
    {
      "name": "ips.tree",
      "title": "Ips Phylogeny",
      "object": "ips.tree",
      "file": "ips.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "log_list",
      "title": "Internal IPS Functions",
      "object": "log_list",
      "file": "log_list.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "clock",
        "tree",
        "tip.dates"
      ],
      "rows": 65,
      "table": true,
      "tojson": true
    },
    {
      "name": "operator_list",
      "title": "Internal IPS Functions",
      "object": "operator_list",
      "file": "operator_list.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "clock",
        "tree",
        "tip.date"
      ],
      "rows": 149,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ips-package",
      "title": "Interfaces to Phylogenetic Software",
      "topics": [
        "ips-package",
        "ips"
      ]
    },
    {
      "page": "aliscore",
      "title": "Masking of Sequence Alignments with ALISCORE",
      "topics": [
        "aliscore"
      ]
    },
    {
      "page": "blastn",
      "title": "Nucleotide-Nucleotide BLAST",
      "topics": [
        "blastn"
      ]
    },
    {
      "page": "code.simple.gaps",
      "title": "Simple Gap/Indel Coding",
      "topics": [
        "code.simple.gaps"
      ]
    },
    {
      "page": "collapseUnsupportedEdges",
      "title": "Collapse Unsupported Edges/Branches in a Phylogeny",
      "topics": [
        "collapseUnsupportedEdges"
      ]
    },
    {
      "page": "combMyTree",
      "title": "Graft Polytomies on Tips of Phylogeny",
      "topics": [
        "combMyTree"
      ]
    },
    {
      "page": "del.miss",
      "title": "Delete Missing Data from DNA Sequences",
      "topics": [
        "del.miss"
      ]
    },
    {
      "page": "deleteGaps",
      "title": "Remove Gap Positions From DNA Sequences",
      "topics": [
        "deleteGaps"
      ]
    },
    {
      "page": "descendants",
      "title": "Descendants of an Internal Node in a Phylogeny",
      "topics": [
        "descendants"
      ]
    },
    {
      "page": "DNAbin2index",
      "title": "Conversion of DNAbin to Index",
      "topics": [
        "DNAbin2index"
      ]
    },
    {
      "page": "EmptyCells",
      "title": "Identify/Delete Spurious Rows and Columns from DNA Alignments",
      "topics": [
        "deleteEmptyCells",
        "EmptyCells",
        "identifyEmptyCells"
      ]
    },
    {
      "page": "oi",
      "title": "Identification of Stem-Lineage-Edges and MRCAs",
      "topics": [
        "eoi",
        "noi",
        "oi"
      ]
    },
    {
      "page": "fixNodes",
      "title": "Standard Node Numbering in Phylo Objects",
      "topics": [
        "fixNodes"
      ]
    },
    {
      "page": "forceEqualTipHeights",
      "title": "Equal Tip Heights",
      "topics": [
        "forceEqualTipHeights"
      ]
    },
    {
      "page": "gblocks",
      "title": "Masking of Sequence Alignments with GBLOCKS",
      "topics": [
        "gblocks"
      ]
    },
    {
      "page": "index2DNAbin",
      "title": "Conversion of Index to DNAbin",
      "topics": [
        "index2DNAbin"
      ]
    },
    {
      "page": "ips.16S",
      "title": "Bark Beetle 16S Sequences",
      "topics": [
        "ips.16S"
      ]
    },
    {
      "page": "ips.28S",
      "title": "Bark Beetle 28S Sequences",
      "topics": [
        "ips.28S"
      ]
    },
    {
      "page": "ips.cox1",
      "title": "Bark Beetle COX1 Sequences",
      "topics": [
        "ips.cox1"
      ]
    },
    {
      "page": "ips.tree",
      "title": "Ips Phylogeny",
      "topics": [
        "ips.tree"
      ]
    },
    {
      "page": "mafft",
      "title": "Sequence Alignment with MAFFT",
      "topics": [
        "mafft"
      ]
    },
    {
      "page": "mafft.merge",
      "title": "Profile Alignment with MAFFT",
      "topics": [
        "mafft.merge"
      ]
    },
    {
      "page": "mrbayes",
      "title": "Bayesian MCMC Tree Search with MrBayes",
      "topics": [
        "mrbayes"
      ]
    },
    {
      "page": "mrbayes.lset",
      "title": "MrBayes model settings",
      "topics": [
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      ]
    },
    {
      "page": "mrbayes.mcmc",
      "title": "MrBayes MCMC settings",
      "topics": [
        "mrbayes.mcmc"
      ]
    },
    {
      "page": "mrbayes.prset",
      "title": "MrBayes prior settings",
      "topics": [
        "mrbayes.prset"
      ]
    },
    {
      "page": "multistate",
      "title": "MULTISTATE",
      "topics": [
        "multistate",
        "multistateMCMC",
        "multistateML"
      ]
    },
    {
      "page": "neighboringPairs",
      "title": "Neighboring Nodes in a Minimum Spanning Tree",
      "topics": [
        "neighboringPairs"
      ]
    },
    {
      "page": "ntip",
      "title": "Numbers of Tips of (Sub)trees",
      "topics": [
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      ]
    },
    {
      "page": "partitionfinder",
      "title": "PartitionFinder",
      "topics": [
        "partitionfinder"
      ]
    },
    {
      "page": "pathd8",
      "title": "PATHd8",
      "topics": [
        "pathd8"
      ]
    },
    {
      "page": "phylo2mafft",
      "title": "Convert Trees for MAFFT",
      "topics": [
        "phylo2mafft"
      ]
    },
    {
      "page": "phylo2mst",
      "title": "Conversion from PHYLO to MST Object",
      "topics": [
        "phylo2mst"
      ]
    },
    {
      "page": "pis",
      "title": "Number of Potentially-Informative Sites",
      "topics": [
        "pis"
      ]
    },
    {
      "page": "prank",
      "title": "PRANK",
      "topics": [
        "prank"
      ]
    },
    {
      "page": "raxml",
      "title": "Maximum Likelihood Tree Estimation with RAxML",
      "topics": [
        "raxml"
      ]
    },
    {
      "page": "raxml.partitions",
      "title": "Partition scheme for RAxML",
      "topics": [
        "raxml.partitions"
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    },
    {
      "page": "rbeauti",
      "title": "XML Input Files for BEAST",
      "topics": [
        "rbeauti"
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    },
    {
      "page": "rc",
      "title": "Reverse-Complement of DNA sequences",
      "topics": [
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    },
    {
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      "title": "Reading Sequence Files",
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        "read.fas",
        "read.nex",
        "read.phy"
      ]
    },
    {
      "page": "read.beast",
      "title": "Read Bayesian Trees",
      "topics": [
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        "read.mrbayes",
        "read.starbeast"
      ]
    },
    {
      "page": "read.beast.table",
      "title": "Extract node data from BEAST chronogram",
      "topics": [
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    },
    {
      "page": "sister",
      "title": "Identification of Sister Nodes and Clades",
      "topics": [
        "sister"
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    },
    {
      "page": "splitIntoClades",
      "title": "Find Monophyletic Subsets in Species Lists",
      "topics": [
        "splitIntoClades"
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    },
    {
      "page": "terminalSisters",
      "title": "Find Pairs of Sister Species",
      "topics": [
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      ]
    },
    {
      "page": "tipHeights",
      "title": "Tip Heights in a Phylogenetic Tree",
      "topics": [
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    },
    {
      "page": "traitRate",
      "title": "Trait-Dependent Shifts in Molecular Rate",
      "topics": [
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    },
    {
      "page": "trimEnds",
      "title": "Trim Alignment Ends",
      "topics": [
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    },
    {
      "page": "unlistFirstLevel",
      "title": "Unlist To First Level Only",
      "topics": [
        "unlistFirstLevel"
      ]
    },
    {
      "page": "write.fas",
      "title": "Write DNA Sequences to File",
      "topics": [
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        "write.nex",
        "write.phy"
      ]
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