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

About the FAQ category [FAQ] (1)
MEGAN5 accession number [FAQ] (2)
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)
Changing Min Score parameter [Usage] (2)
Extract functional information [Usage] (2)
Read R has a top hit to taxon T, but taxon T does not turn up in the taxonomy tree [Usage] (1)