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| RADami-package | Phylogenetic Analysis of RADseq Data |
| compare.all.trees | Compare all trees in a treeset, and return a matrix (lower diagonal only) indicating which pairwise comparisons are identical |
| consensus.pyRAD | Generate a consensus sequence for each of the loci in a pyRAD.loci object |
| filter.by | Identify names of loci for which at the requested taxa are present, either all or some number of them |
| gen.RAD.loci.datasets | Generate datasets for partitioned RAD analysis |
| genotypes.pyRAD.loci | Generates genotypes from a 'subset.pyRAD.loci' object |
| genTrees | Generate permuted trees using rNNI or rtree, and check for uniqueness. |
| get.raxml.siteLikelihoods | Read likelihoods from a RAxML_perSiteLLs file |
| get.raxml.treeLikelihoods | Extract likelihoods from a RAxML info file |
| grab.pyRAD.locus | Extract sequence data for one or a few loci |
| lengths.report | Return the lengths of all loci in a pyRAD.loci object |
| locus.dist | Generate a pairwise similarity matrix for individuals based on locus-sharing patterns |
| match.lnL.to.trees | Match the likelihoods returned on a subset of trees for numerous loci to the trees originally input |
| oak.rads | 101-locus RAD dataset, in 'pyRAD.loci' format |
| oak.tree | 28-tip oak phylogeny, in 'phylo' format |
| overlap.report | Generates a report on locus overlap between pairs of samples named in a structured fashion |
| pairwise.fst.loci | Returns pairwise FST list for groups of individuals |
| plot.locus.dist | Plot a phylogeny with a graphical representation of locus sharing |
| plot.partitionedRAD | Plot a 'partitionedRAD' object |
| plot.rankedPartitionedRAD | Plot a 'rankedPartitionedRAD' object |
| print.pyRAD.loci | Print method for 'pyRAD.loci' objects |
| rad2mat | Generates a matrix of sequences from a 'pyRAD.loci' object |
| rad2phy | Export a 'rad.mat' object to a phylip file |
| RADami | Phylogenetic Analysis of RADseq Data |
| rank.partitionedRAD | Bin trees into 'suppported' or 'disfavored' by locus. |
| read.pyRAD | Read in data from pyRAD |
| rtreePhylo | Generate random trees using an input tree to get taxon names and tips |
| subset.pyRAD.loci | Subsets a 'pyRAD.loci' object |
| summary.pyRAD.loci | Summary method for 'pyRAD.loci' objects |
| tidyName | Clean up a name |
| write.DNAStringSet | Writes a sequence matrix to phylip format |