RADami: Phylogenetic Analysis of RADseq Data

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

Install the latest version of this package by entering the following in R:
AuthorAndrew Hipp [aut, cre], Klaus Schliep [ctb]
Date of publication2017-02-11 10:04:29
MaintainerAndrew 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...

genotypes.pyRAD.loci: Generates genotypes from a 'subset.pyRAD.loci' object

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

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...

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...

pairwise.fst: Returns pairwise FST list for groups of individuals

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: 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

tidyName: Clean up a name

write.DNAStringSet: Writes a sequence matrix to phylip format


compare.all.trees Man page
consensus.pyRAD Man page
filter.by Man page
genotypes.pyRAD.loci Man page
gen.RAD.loci.datasets Man page
genTrees Man page
get.raxml.siteLikelihoods Man page
get.raxml.treeLikelihoods Man page
grab.pyRAD.locus Man page
lengths.report Man page
locus.dist Man page
match.lnL.to.trees Man page
oak.rads Man page
oak.tree Man page
overlap.report Man page
pairwise.fst.loci Man page
plot.locus.dist Man page
plot.partitionedRAD Man page
plot.rankedPartitionedRAD Man page
print.pyRAD.loci Man page
rad2mat Man page
rad2phy Man page
RADami Man page
RADami-package Man page
rank.partitionedRAD Man page
read.pyRAD Man page
rtreePhylo Man page
subset.pyRAD.loci Man page
summary.pyRAD.loci Man page
tidyName Man page
write.DNAStringSet Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.