RADami-package          R Package for 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
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
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
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
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
write.DNAStringSet      Writes a sequence matrix to phylip format
