DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
dDocent was designed as a scripted software pipeline made for analyzing double digest RAD (Peterson et al. 2012) or ezRAD (Toonen et al. 2013) data in highly polymorphic marine species.
DESMAN (De novo Extraction of Strains from MetAgeNomes) enables strain inference from frequency counts on contigs across multiple samples.
The Dextractor commands allow one to pull exactly and only the information needed for assembly and reconstruction from the source HDF5 files produced by the PacBio RS II sequencer, or from the source BAM files produced by the PacBio Sequel sequencer.
DIAMOND is a protein sequence aligner.
DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting)
dRep can rapidly and accurately compare a list of genomes in a pair-wise manner.
DSK is a k-mer counter for reads or genomes. The DSK software comes with the GATB module.