AmphoraNet
ClaMS
Clark
CoMet-Universe
EBI Metagenomics
EstimateS
E-vident
Fantom
FLASh
Genometa
Glimmer-MG
GOTTCHA
IMG/M
[iPlant] (https://pods.iplantcollaborative.org/wiki/display/WiNGS/Scalable+metagenomic+analysis+using+iPlant)
Kraken
MEGAN6
MetaABC
METAGENassist
metagenomeSeq
Meta-IDBA
metaMicrobesOnline
MetAMOS
MetaPhlAn
MetaPhyler
Metarep
MetaVelvet
METAVIR
Mothur
My Taxa
One Codex
Panda
PEAR
PhymmlBL
QIIME
Real Time Metagenomics
Ribosomal Database Project
SMASHCommunity
Taxator-tk
VIROME
Xander
ZORRO