RADami: R Package for Phylogenetic Analysis of RADseq Data

This package implements import, export, manipulation, visualization, and downstream (post-clustering) analysis of RADseq data, integrating with the pyRAD package by Deren Eaton.

AuthorAndrew L. Hipp <ahipp@mortonarb.org>
Date of publication2014-03-03 12:10:23
MaintainerAndrew L. Hipp <ahipp@mortonarb.org>

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Man pages

compare.all.trees: Compare all trees in a treeset, and return a matrix (lower...

consensus.pyRAD: Generate a consensus sequence for each of the loci in a...

filter.by: Identify names of loci for which at the requested taxa are...

gen.RAD.loci.datasets: Generate datasets for partitioned RAD analysis

genTrees: Generate permuted trees using rNNI or rtree, and check for...

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...

match.lnL.to.trees: Match the likelihoods returned on a subset of trees for...

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...

plot.locus.dist: Plot a phylogeny with a graphical representation of locus...

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-package: R Package for 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...

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

Files in this package

RADami/R/filter.by.R RADami/R/rank.partitionedRAD.R RADami/R/write.DNAStringSet.R RADami/R/rtreePhylo.R RADami/R/get.raxml.treeLikelihoods.R RADami/R/plot.partitionedRAD.R RADami/R/get.raxml.siteLikelihoods.R RADami/R/print.pyRAD.loci.R RADami/R/genTrees.R RADami/R/rad2mat.R RADami/R/gen.RAD.loci.datasets.R RADami/R/plot.rankedPartitionedRAD.R RADami/R/compare.all.trees.R RADami/R/consensus.pyRAD.R RADami/R/lengths.report.R RADami/R/summary.pyRAD.loci.R RADami/R/subset.pyRAD.loci.R RADami/R/locus.dist.R RADami/R/plot.locus.dist.R RADami/R/unique.multiPhylo.R RADami/R/read.pyRAD.R RADami/R/overlap.report.R RADami/R/match.lnL.to.trees.R RADami/R/rad2phy.R
RADami/man/rtreePhylo.Rd RADami/man/oak.tree.Rd RADami/man/rad2phy.Rd RADami/man/rad2mat.Rd RADami/man/overlap.report.Rd RADami/man/gen.RAD.loci.datasets.Rd RADami/man/get.raxml.siteLikelihoods.Rd RADami/man/consensus.pyRAD.Rd RADami/man/summary.pyRAD.loci.Rd RADami/man/write.DNAStringSet.Rd RADami/man/locus.dist.Rd RADami/man/subset.pyRAD.loci.Rd RADami/man/match.lnL.to.trees.Rd RADami/man/RADami-package.Rd RADami/man/compare.all.trees.Rd RADami/man/plot.locus.dist.Rd RADami/man/genTrees.Rd RADami/man/lengths.report.Rd RADami/man/filter.by.Rd RADami/man/rank.partitionedRAD.Rd RADami/man/print.pyRAD.loci.Rd RADami/man/read.pyRAD.Rd RADami/man/oak.rads.Rd RADami/man/get.raxml.treeLikelihoods.Rd RADami/man/plot.partitionedRAD.Rd RADami/man/plot.rankedPartitionedRAD.Rd

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