Man pages for RADami
Phylogenetic Analysis of RADseq Data

compare.all.treesCompare all trees in a treeset, and return a matrix (lower...
consensus.pyRADGenerate a consensus sequence for each of the loci in a...
filter.byIdentify names of loci for which at the requested taxa are...
genotypes.pyRAD.lociGenerates genotypes from a 'subset.pyRAD.loci' object
gen.RAD.loci.datasetsGenerate datasets for partitioned RAD analysis
genTreesGenerate permuted trees using rNNI or rtree, and check for...
get.raxml.siteLikelihoodsRead likelihoods from a RAxML_perSiteLLs file
get.raxml.treeLikelihoodsExtract likelihoods from a RAxML info file
grab.pyRAD.locusExtract sequence data for one or a few loci
lengths.reportReturn the lengths of all loci in a pyRAD.loci object
locus.distGenerate a pairwise similarity matrix for individuals based...
match.lnL.to.treesMatch the likelihoods returned on a subset of trees for...
oak.rads101-locus RAD dataset, in 'pyRAD.loci' format
oak.tree28-tip oak phylogeny, in 'phylo' format
overlap.reportGenerates a report on locus overlap between pairs of samples...
pairwise.fstReturns pairwise FST list for groups of individuals
plot.locus.distPlot a phylogeny with a graphical representation of locus...
plot.partitionedRADPlot a 'partitionedRAD' object
plot.rankedPartitionedRADPlot a 'rankedPartitionedRAD' object
print.pyRAD.lociPrint method for 'pyRAD.loci' objects
rad2matGenerates a matrix of sequences from a 'pyRAD.loci' object
rad2phyExport a 'rad.mat' object to a phylip file
RADami-packagePhylogenetic Analysis of RADseq Data
rank.partitionedRADBin trees into 'suppported' or 'disfavored' by locus.
read.pyRADRead in data from pyRAD
rtreePhyloGenerate random trees using an input tree to get taxon names...
subset.pyRAD.lociSubsets a 'pyRAD.loci' object
summary.pyRAD.lociSummary method for 'pyRAD.loci' objects
tidyNameClean up a name
write.DNAStringSetWrites a sequence matrix to phylip format
RADami documentation built on May 30, 2017, 8:23 a.m.