Man pages for lliu1871/phybase
Basic functions for phylogenetic analysis
| alignment.mle.remove | alignment.mle.remove sequences |
| alignment.reference.remove | alignment.reference.remove removes sequences |
| alignment.site.summary | summary statistics of sequences |
| alignment.summary | summary statistics of sequences |
| alignment.trim | alignment.trim sequences |
| bootstrap | Bootstrap sequences |
| bootstrap.mulgene | Bootstrap sequences from multiple loci |
| control.mpest | generate a control file for mpest |
| dat.coaltree | species tree and gene trees |
| dat.finch | multilocus sequence data |
| dat.modelcode | substitution model code |
| dat.unrootedtree | unrooted trees |
| del.brlens | Delete branch lengths from trees |
| del.comments | Delete comments |
| del.node | Delete a node from the tree |
| dist.dna | Calculate pairwise distances among DNA sequences |
| dist.internode | find the distance of two taxa |
| dist.species | Calculate pairwise distances among species |
| dist.taxa | Calculate all pairwise distances among taxa in the tree |
| file.beast2phylip | convert beast files to phylip files |
| file.concatData | concatenate sequences from multiple files |
| file.fasta2phylip | convert fasta files to phylip files |
| file.nexus2phylip | convert nexus files to phylip files |
| file.phylip2nexus | convert phylip files to nexus files |
| file.separateGeneData | separate the concatenated sequences into individual genes |
| is.clock | Is a clock tree or not |
| is.rootedtree | Is the tree rooted or not |
| loglike.coal | loglikelihood of the species tree, i.e., Rannala and Yang... |
| loglike.triple | Loglikehood of Triples |
| node.height | Calculate node height |
| parse.modeltest | parse modeltest outputs |
| parse.phyml | parse phyml outputs |
| parse.raxml | parse raxml outputs |
| phybase-package | Basic functions for Phylogenetic trees |
| read.dna.seq | Read sequences from files |
| read.tree.nodes | Read tree nodes |
| read.tree.string | Read tree strings from a tree file |
| run.modeltest | run modeltest |
| run.mpest | run mpest |
| run.seqgen | run seq-gen |
| sim.coal.mpest | Simulate gene trees from the mpest tree under the coalescent... |
| sim.coaltree | Simulate a coalescence tree |
| sim.coaltree.sp | simulate a gene tree from the species tree |
| sim.coaltree.sp.mu | Simulate a gene tree from the non-clock species tree model |
| sim.dna | Simulate DNA sequences from substitution models |
| sim.SeqfromSp | simulate DNA sequences from a species tree |
| site.pattern | Site patterns |
| site.summary | summarize alignments |
| species.name | Species names in a tree string |
| sptree.alleletable | Create a sequence-species relationship |
| sptree.maxtree | Maximum Tree |
| sptree.njst | calculate the sptree.njst tree |
| sptree.star | Build a STAR tree |
| sptree.steac | Build a STEAC tree |
| test.2sptree | testing if two species trees are significantly different |
| test.equalgenetree | testing if gene trees are identical |
| test.hybrid | testing if there are two species trees |
| test.submodel.valid.phyml | model validation of the substitution models |
| test.submodel.valid.raxml | model validation of the substitution models |
| tree.brlens | summarizing branch lengths |
| tree.consensus | consensus tree |
| tree.distance | tree distance |
| tree.name2node | Replace species names by their node numbers |
| tree.noclock2clock | Convert a non-clocklike tree to a clocklike tree |
| tree.node2name | Replace node numbers by species names in a tree string |
| tree.partition | partition a tree |
| tree.plot | tree plot |
| tree.probdist | tree.probdist |
| tree.subtree | Subtree |
| tree.upgma | tree.upgma tree |
| write.dna.seq | Write sequences to a Nexus file |
| write.seq.phylip | write concatenated sequences to a file |
| write.subtree | Write a sub-tree into a string |
| write.tree.string | Write a tree file |
