Generates genotypes from a
Generate datasets for partitioned RAD analysis
Generate a consensus sequence for each of the loci in a pyRAD.loci object
Identify names of loci for which at the requested taxa are present,
get.raxml.siteLikelihoods
Return the lengths of all loci in a pyRAD.loci object
Compare all trees in a treeset, and return a matrix (lower diagonal only) indicating which pairwise comparisons are identical
Extract sequence data for one or a few loci
get.raxml.treeLikelihoods
Extract likelihoods from a RAxML info file
Returns pairwise FST list for groups of individuals
Generate a pairwise similarity matrix for individuals based on locus-sharing patterns
Print method for
plot.rankedPartitionedRAD
Plot a
Plot a phylogeny with a graphical representation of locus sharing
28-tip oak phylogeny, in
101-locus RAD dataset, in
Generates a report on locus overlap between pairs of samples named in a structured fashion
Match the likelihoods returned on a subset of trees for numerous loci to the trees originally input
Plot a
Generates a matrix of sequences from a
Summary method for
Writes a sequence matrix to phylip format
Export a
Phylogenetic Analysis of RADseq Data
Subsets a
Bin trees into 'suppported' or 'disfavored' by locus.
Generate random trees using an input tree to get taxon names and tips
Read in data from pyRAD