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.

The EDTA package (Extensive de novo TE Annotator) was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.

eggNOG-mapper is a tool for fast functional annotation of novel sequences.

EvidentialGene (also called evigene) is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.

Exonerate is a generic tool for pairwise sequence comparison.