I’m using MEGAN 5.10.1 and the default LCA parameters seem different from what’s suggested in the manual.
The first is Min Support Percent, which is off and Min Support is 1, meaning only 1 read is necessary to support a taxa. In the manual it says the default is 0.1% Min Support Percent.
The Min Complexity filter is by default off, but the manual suggests that a value of 0.3 should be used.
The min support and min support percent filters are tricky to use. I would suggest to use min support percent 0.1%, but this also depends on your dataset and the type of question that you are asking. Filtering using min support reduces the spread of taxa that you will see, but of course if your goal is to search for specific low abundance taxa, then you should set this value to something much smaller.
Whether you need to use the min complexity filter or not will depend on what tool you used to compute the initial alignments. Blast or DIAMOND do there own complexity filtering, so in these cases using MEGAN’s filter may not be necessary, but on the other hand, it won’t do any harm (except that it will make processing of files take longer).
So, in both cases, no 100% straight answer, I’m sorry…