API for lliu1871/phybase
Basic functions for phylogenetic analysis
| Global functions | |
|---|---|
| .ChangeBrlen | Source code |
| .FindSpnodeDownGenenode | Source code |
| .ambisite | Source code |
| .ancestor | Source code Source code Source code |
| .basefreq | Source code |
| .concatData | Source code |
| .dist.tip.root | Source code |
| .gc | Source code |
| .gc.variance | Source code |
| .gc_12pos | Source code |
| .gc_12pos.variance | Source code |
| .gc_3pos | Source code |
| .gc_3pos.variance | Source code |
| .getcoaltime | Source code |
| .getncoal | Source code |
| .informsite | Source code |
| .is.ambisite | Source code |
| .is.informsite | Source code |
| .is.segsite | Source code |
| .mrca.2nodes | Source code Source code |
| .mutation_exp | Source code |
| .node.height | Source code |
| .numtaxa | Source code |
| .offspring.nodes | Source code Source code Source code Source code |
| .offspring.nodes.string | Source code Source code Source code Source code |
| .offspring.species | Source code Source code |
| .pairfreq | Source code Source code |
| .patternfreq | Source code Source code |
| .rank.nodes | Source code |
| .rdirichlet | Source code |
| .segsite | Source code |
| .seqlength | Source code |
| .sim.nucleotide | Source code |
| .sortmat | Source code |
| .swap.nodes | Source code |
| .triplenumber | Source code |
| .triplepara | Source code |
| .unroottree | Source code Source code |
| PhyBase | Man page |
| `dist.dna` | Source code |
| `read.dna.seq` | Source code |
| `sim.coaltree.sp` | Source code |
| `sim.coaltree` | Source code |
| `sim.dna` | Source code |
| `sptree.maxtree` | Source code |
| `tree.plot` | Source code |
| alignment.mle.remove | Man page |
| alignment.reference.remove | Man page |
| alignment.site.summary | Man page |
| alignment.summary | Man page |
| alignment.trim | Man page |
| bootstrap | Man page |
| bootstrap.mulgene | Man page |
| control.mpest | Man page |
| dat.coaltree | Man page |
| dat.finch | Man page |
| dat.modelcode | Man page |
| dat.unrootedtree | Man page |
| del.brlens | Man page |
| del.comments | Man page |
| del.node | Man page |
| dist.dna | Man page |
| dist.internode | Man page |
| dist.species | Man page |
| dist.taxa | Man page |
| file.beast2phylip | Man page |
| file.concatData | Man page |
| file.fasta2phylip | Man page |
| file.nexus2phylip | Man page |
| file.phylip2nexus | Man page |
| file.separateGeneData | Man page |
| is.clock | Man page |
| is.rootedtree | Man page |
| loglike.coal | Man page |
| loglike.triple | Man page |
| node.height | Man page |
| parse.modeltest | Man page |
| parse.phyml | Man page |
| parse.raxml | Man page |
| read.dna.seq | Man page |
| read.tree.nodes | Man page Source code |
| read.tree.string | Man page |
| run.modeltest | Man page |
| run.mpest | Man page |
| run.seqgen | Man page Source code |
| sim.SeqfromSp | Man page |
| sim.coal.mpest | Man page |
| sim.coaltree | Man page |
| sim.coaltree.sp | Man page |
| sim.coaltree.sp.mu | Man page |
| sim.dna | Man page |
| site.pattern | Man page |
| site.summary | Man page |
| species.name | Man page |
| sptree.alleletable | Man page |
| sptree.maxtree | Man page |
| sptree.njst | Man page |
| sptree.star | Man page |
| sptree.steac | Man page |
| test.2sptree | Man page |
| test.equalgenetree | Man page |
| test.hybrid | Man page |
| test.submodel.valid.phyml | Man page |
| test.submodel.valid.raxml | Man page |
| tree.brlens | Man page |
| tree.consensus | Man page |
| tree.distance | Man page |
| tree.name2node | Man page |
| tree.noclock2clock | Man page |
| tree.node2name | Man page |
| tree.partition | Man page |
| tree.plot | Man page |
| tree.probdist | Man page |
| tree.subtree | Man page |
| tree.upgma | Man page |
| write.dna.seq | Man page |
| write.seq.phylip | Man page |
| write.subtree | Man page |
| write.tree.string | Man page |
