I am using the blast2rma command-line tool to meganize my files. Does anyone have a list of the flags that we can use with this command? I have been using -g2t for taxonomy, -a2eggnog for eggNOG, etc., but from what I see there are many more.
I just started using the latest version of MEGAN community edition (v6.8.18), in place of version 6.4.5 that I was using earlier, and it gave me an error for -mag flag. So it’ll be really useful to have a list of flags for blast2rma command-line tool.