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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