Function reference • phruta

Mining genbank

Functions to mine genbank

gene.sampling.retrieve(): Retrieve the distribution of genes for given organism in genbank

acc.table.retrieve(): Retrieve accession numbers and titles for a given combination of species and genes in genbank

sq.retrieve.direct(): Retrieve sequences from genbank

sq.retrieve.indirect(): Retrieve sequences from genbank based on a dataset of accession numbers

Pre-processing sequences

Functions for pre-processing sequences.

sq.add(): Add local sequences to previously downloaded sequences

sq.curate(): Curate sequences from genbank

sq.aln(): Align sequences

Inferring and exploring phylogenies

Functions for inferring and exploring phylogenetic trees

tree.constraint(): Tree inference under RAxML

tree.dating(): Tree dating under treePL or

tree.raxml(): Tree inference under RAxML

tree.roguetaxa(): RogueNaRok within phruta

sq.partitionfinderv1(): Run Partitionfinder v.1