Command-line usage Frequently asked question about MEGAN Ultimates command-line mode.
Usage In this category we collect typical usage questions and SOPs (Standard Operating Procedures) which help you getting your analysis started.
Technical Problems This section of the FAQ includes frequently occurring technical problems.

About the FAQ category [FAQ] (1)
Unable to open MEGAN [Technical Problems] (5)
Changing Input Domination Filter [FAQ] (7)
Command line on a remote server [Command-line usage] (5)
MEGAN5 accession number [FAQ] (3)
Usage of Megan version6 [FAQ] (2)
Problem running MEGAN v6.10.3 on Ubuntu 16.04.3 LTS [Technical Problems] (4)
LCA parameters to keep best hit only for taxonomic annotation [FAQ] (3)
MALT Index issues [FAQ] (8)
Megan6_KEGG data analysis [Technical Problems] (1)
Compare 100+ samples using command-line [Command-line usage] (3)
No KEGG or EGGNOG assignment [Command-line usage] (2)
Running scripts [FAQ] (2)
Where can I find example files to try MEGAN? [Usage] (10)
Daa2rma abin file read error [Command-line usage] (2)
List of blast2rma command-line tool flags and attributes? [Command-line usage] (2)
Does MEGAN COG/eggNOG reflect arCOGs and KOGs as well? [Usage] (5)
Last or DIAMOND? [FAQ] (10)
How to use my own taxonomic or functional classification in MEGAN? [Usage] (3)
How MEGAN normalizes the data [FAQ] (4)
Gene Centric Alignment [FAQ] (5)
Megan Usage troubleshooting [Usage] (2)
Megan6__6_7 not working on Ubuntu 14.04 [Technical Problems] (2)
Export KEGG annotation [Command-line usage] (4)
Meganize Diamond DAA to RMA files [Command-line usage] (4)
Problem importing BlastXML files to MEGAN (6.5.10) [Technical Problems] (4)
BIOM export to load in R [Technical Problems] (2)
Megan6_5_5 not working on macos [Technical Problems] (3)
All the imported reads were recongnized as "no hits" in functional analysis [FAQ] (1)
How can I use highlight Differences? [Technical Problems] (1)