Changing Input Domination Filter

How do you change the input domination filter (specifically, MinPercentCoverToStronglyDominate and defaultTopPercentScoreToDominate which are both set to 90) in the Community Edition of MEGAN6 ?

This feature is currently missing in the Community Edition. I will add it in the next release.

As a workaround, edit the MEGAN properties file and add lines like this


to change the MinPercentCoverToStronglyDominate from 90 (default) to 70 and to change the TopPercentScoreToStronglyDominate value from 90 (default) to 80, say.

Linux and Windows: the properties file is contained in your home directory and is called .Megan.def
MacOS: the properties file is here: ~/Library/Preferences/Megan.def

The names mentioned here are slightly different than what MEGAN reports, but they are correct.

Note that there is a similarly named parameter MinPercentCoverToDominate.
This is used only in the export of GFF3 format. The GFF3 export needs improvement and we are currently working on that.

find . -name “Megan.def”
did not yield any results

Note that the linux name starts with a dot: .Megan.def
The linux file is here: ~/.Megan.def
That is, it is a hidden file in your home directory, use “ls -f” in your home directory to list all hidden files

But I’m using a Mac OS

In your home directory, type this:

ls Library/Preferences/Megan.def

This will list the file.