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  "Title": "Interfaces to Phylogenetic Software in R",
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  "Description": "Functions that wrap popular phylogenetic software for\nsequence alignment, masking of sequence alignments, and\nestimation of phylogenies and ancestral character states.",
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    "read.mrbayes",
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    "read.phy",
    "read.starbeast",
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    "sister",
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    "terminal.clades",
    "terminalSisters",
    "tipHeights",
    "traitRate",
    "trimEnds",
    "unlistFirstLevel",
    "unresolve.clade",
    "write.fas",
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    "write.phy"
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      ],
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      "table": false,
      "tojson": false
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      ],
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      "tojson": true
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      "table": true,
      "tojson": true
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    {
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      "title": "Interfaces to Phylogenetic Software",
      "topics": [
        "ips-package",
        "ips"
      ]
    },
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      "title": "Masking of Sequence Alignments with ALISCORE",
      "topics": [
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      "title": "Nucleotide-Nucleotide BLAST",
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      "title": "Simple Gap/Indel Coding",
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      "topics": [
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      ]
    },
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      "title": "Graft Polytomies on Tips of Phylogeny",
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      "title": "Delete Missing Data from DNA Sequences",
      "topics": [
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      ]
    },
    {
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      "title": "Remove Gap Positions From DNA Sequences",
      "topics": [
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    },
    {
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      "title": "Descendants of an Internal Node in a Phylogeny",
      "topics": [
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      ]
    },
    {
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      "title": "Conversion of DNAbin to Index",
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    },
    {
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        "identifyEmptyCells"
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      "title": "Identification of Stem-Lineage-Edges and MRCAs",
      "topics": [
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        "noi",
        "oi"
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    },
    {
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      "title": "Standard Node Numbering in Phylo Objects",
      "topics": [
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      "title": "Equal Tip Heights",
      "topics": [
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      "title": "Profile Alignment with MAFFT",
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      "title": "Bayesian MCMC Tree Search with MrBayes",
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      "title": "MULTISTATE",
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        "multistateMCMC",
        "multistateML"
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