{ "_id": "6a104e0facfb0bcc41ca08cd", "Package": "phybase", "Type": "Package", "Title": "Basic functions for phylogenetic analysis", "Version": "1.1", "Date": "2008-03-25", "Author": "Liang Liu", "Maintainer": "Liang Liu ", "Description": "This package provides functions to read, write,\nmanipulate, estimate, and summarize phylogenetic trees\nincluding species trees which contain not only the topology and\nbranch lengths but also population sizes. The input/output\nfunctions can read tree files in which trees are presented in\nparenthetic format. The trees are read in as a string and then\ntransformed to a matrix which describes the relationship of\nnodes and branch lengths. The nodes matrix provides an easy\naccess for developers to further manipulate the tree, while the\ntree string provides interface with other phylogenetic R\npackages such as \"ape\". The input/output functions can also be\nused to change the format of tree files between NEXUS and\nPHYLIP. Some basic functions have already been established in\nthe package for manipulating trees such as deleting and\nswapping nodes, rooting and unrooting trees, changing the root\nof the tree. The package also includes functions such as\n\"consensus\", \"coaltime, \"popsize\", \"treedist\" for summarizing\nphylogenetic trees, calculating the coalescence time,\npopulation size, and tree distance. The function maxtree is\nbuilt in the package to esimtate the species tree from multiple\ngene trees.", "License": "GPL (>= 2)", "Packaged": { "Date": "2026-05-10 06:37:02 UTC", "User": "root" }, "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2008-03-25 00:00:00 UTC", "RemoteUrl": "https://github.com/cran/phybase", "RemoteRef": "HEAD", "RemoteSha": "d8ea06b72e176a07c0164e7e9f7ea66966b9f467", "NeedsCompilation": "yes", "MD5sum": "81e10347cceb97797eb3545e32f7a2c3", "_user": "phylotastic", "_type": "src", "_file": "phybase_1.1.tar.gz", "_fileid": "4039494ef732a71dcfa36dd55bff60bde1b8f8e01cc53f36511a0c78469cb58f", "_filesize": 261367, "_sha256": "4039494ef732a71dcfa36dd55bff60bde1b8f8e01cc53f36511a0c78469cb58f", "_created": "2026-05-10T06:37:02.000Z", "_published": "2026-05-22T12:37:35.660Z", "_distro": "noble", "_jobs": [ { "job": 77380794245, "time": 120, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "6901644367" }, { "job": 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"role": "Depends" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 2, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phybase" }, "_searchresults": 83, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/phybase.html", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "1.1", "date": "2012-10-29" } ], "_exports": [ "ancandtime", "ancestor", "bootstrap", "bootstrap.mulgene", "change.root", "ChangeBrlen", "coal.sptree", "coaltime", "consense", "del.node", "FindSpnodeDownGenenode", "genetree.vector", "getcoaltime", "getncoal", "is.clock", "is.rootedtree", "maxtree", "mrca.2nodes", "mrca.nodes", "mutation_exp", "name2node", "noclock2clock", "node.height", "node2name", "offspring.nodes", 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"character" ], "fields": [], "table": false, "tojson": true }, { "name": "unrooted.tree", "title": "An example of unrooted trees", "object": "unrooted.tree", "file": "unrooted.tree.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "phybase-package", "title": "Basic functions for Phylogenetic trees", "topics": [ "PhyBase" ] }, { "page": "ancandtime", "title": "Get ancestors and their divergence times", "topics": [ "ancandtime" ] }, { "page": "ancestor", "title": "Find the ancestral nodes of a node", "topics": [ "ancestor" ] }, { "page": "bootstrap", "title": "Bootstrap sequences", "topics": [ "bootstrap" ] }, { "page": "bootstrap.mulgene", "title": "Bootstrap sequences from multiple loci", "topics": [ "bootstrap.mulgene" ] }, { "page": "change.root", "title": "Change tree root", "topics": [ "change.root" ] }, { "page": "ChangeBrlen", "title": "Change the branch length", "topics": [ "ChangeBrlen" ] }, { "page": "coal.sptree", "title": 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"maxtree" ] }, { "page": "mrca.2nodes", "title": "Find the most recent common ancestor of two nodes", "topics": [ "mrca.2nodes" ] }, { "page": "mrca.nodes", "title": "Find the most recent common ancestor of multiple nodes", "topics": [ "mrca.nodes" ] }, { "page": "mutation_exp", "title": "Generate mutation rates for populations in the species tree", "topics": [ "mutation_exp" ] }, { "page": "name2node", "title": "Replace species names by their node numbers", "topics": [ "name2node" ] }, { "page": "noclock2clock", "title": "Convert a non-clocklike tree to a clocklike tree", "topics": [ "noclock2clock" ] }, { "page": "node.height", "title": "Calculate node height", "topics": [ "node.height" ] }, { "page": "node2name", "title": "Replace node numbers by species names in a tree string", "topics": [ "node2name" ] }, { "page": "offspring.nodes", "title": "Find the offspring nodes", "topics": [ "offspring.nodes" ] }, { "page": "offspring.nodes.string", "title": "Find offspring nodes (internal use only)", "topics": [ "offspring.nodes.string" ] }, { "page": "offspring.species", "title": "Find the species nodes", "topics": [ "offspring.species" ] }, { "page": "pair.dist", "title": "Calculate all pairwise distances among taxa in the tree", "topics": [ "pair.dist" ] }, { "page": "pair.dist.dna", "title": "Calculate pairwise distances among DNA sequences", "topics": [ "pair.dist.dna" ] }, { "page": "pair.dist.mulseq", "title": "Calculate pairwise distances among species", "topics": [ "pair.dist.mulseq" ] }, { "page": "partition.tree", "title": "partition a tree", "topics": [ "partition.tree" ] }, { "page": "plottree", "title": "Write a tree file", "topics": [ "plottree" ] }, { "page": "popsize", "title": "Population size of the most recent common ancestor of two nodes", "topics": [ "popsize" ] }, { "page": "populationMutation", "title": "Change branch lengths of a gene tree in the non-clocklike species tree model (internal use only)", "topics": [ "populationMutation" ] }, { "page": "postdist.tree", "title": "Calculate posterior probabilities of trees", "topics": [ "postdist.tree" ] }, { "page": "rank.nodes", "title": "Node ranks (internal use only)", "topics": [ "rank.nodes" ] }, { "page": "rannalandyang", "title": "Rannala and Yang's formula", "topics": [ "rannalandyang" ] }, { "page": "rdirichlet", "title": "Generate random numbers from the dirichlet distribution", "topics": [ "rdirichlet" ] }, { "page": "read.dna.seq", "title": "Read sequences from files", "topics": [ "read.dna.seq" ] }, { "page": "read.tree.nodes", "title": "Read tree nodes", "topics": [ "read.tree.nodes" ] }, { "page": "read.tree.string", "title": "Read tree strings from a tree file", "topics": [ "read.tree.string" ] }, { "page": "root.tree", "title": "Root a tree", "topics": [ "root.tree" ] }, { "page": "rooted.tree", "title": "An example of rooted trees", "topics": [ "rooted.tree" ] }, { "page": "rootoftree", "title": "Root of a tree", "topics": [ "rootoftree" ] }, { "page": "sctree", "title": "Shallowest Coalescence Tree", "topics": [ "sctree" ] }, { "page": "sim.coaltree", "title": "Simulate a coalescence tree", "topics": [ "sim.coaltree" ] }, { "page": "sim.coaltree.sp", "title": "simulate a gene tree from the species tree", "topics": [ "sim.coaltree.sp" ] }, { "page": "sim.coaltree.sp.mu", "title": "Simulate a gene tree from the non-clock species tree model", "topics": [ "sim.coaltree.sp.mu" ] }, { "page": "sim.dna", "title": "Simulate DNA sequences from substitution models", "topics": [ "sim.dna" ] }, { "page": "simnucleotide", "title": "Intrinsic function used in sim.dna", "topics": [ "simnucleotide" ] }, { "page": "simSeqfromSp", "title": "simulate DNA sequences from a species tree", "topics": [ "simSeqfromSp" ] }, { "page": "site.pattern", "title": "Site patterns", "topics": [ "site.pattern" ] }, { "page": "sortmat", "title": "Sort a matrix", "topics": [ "sortmat" ] }, { "page": "species.name", "title": "Species names in a tree string", "topics": [ "species.name" ] }, { "page": "spstructure", "title": "Create a sequence-species relationship", "topics": [ "spstructure" ] }, { "page": "sptree", "title": "A species tree", "topics": [ "sptree" ] }, { "page": "star.sptree", "title": "Build a STAR tree", "topics": [ "star.sptree" ] }, { "page": "steac.sptree", "title": "Build a STEAC tree", "topics": [ "steac.sptree" ] }, { "page": "subtree", "title": "Subtree", "topics": [ "subtree" ] }, { "page": "subtree.length", "title": "Calculate total branch length of a tree", "topics": [ "subtree.length" ] }, { "page": "swap.nodes", "title": "Swap two nodes", "topics": [ "swap.nodes" ] }, { "page": "treedist", "title": "Distance between two trees", "topics": [ "treedist" ] }, { "page": "tripleloglike", "title": "Loglikehood of Triples", "topics": [ "tripleloglike" ] }, { "page": "triplenumber", "title": "Internal function", "topics": [ "triplenumber" ] }, { "page": "triplepara", "title": "Internal function", "topics": [ "triplepara" ] }, { "page": "tripleProb", "title": "Probability of a set of rooted triples", "topics": [ "tripleProb" ] }, { "page": "unrooted.tree", "title": "An example of unrooted trees", "topics": [ "unrooted.tree" ] }, { "page": "unroottree", "title": "Unroot a tree", "topics": [ "unroottree" ] }, { "page": "upgma", "title": "UPGMA tree", "topics": [ "upgma" ] }, { "page": "write.dna", "title": "Write sequences to a Nexus file", "topics": [ "write.dna" ] }, { "page": "write.subtree", "title": "Write a sub-tree into a string", "topics": [ "write.subtree" ] }, { "page": "write.tree.string", "title": "Write a tree file", "topics": [ "write.tree.string" ] } ], "_rundeps": [ "ape", "digest", "lattice", "Matrix", "nlme", "Rcpp" ], "_score": 1.919078092376074, "_indexed": false, "_nocasepkg": "phybase", "_universes": [ "phylotastic" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1", "date": "2026-05-10T06:38:55.000Z", "distro": "noble", "arch": "aarch64", "commit": 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