What does hhfilter exactly do ?

[TaoDFang]

Hi,

First, thanks a lot for providing this great tool. May I ask something about hhfilter ? I'm confused about some input arguments while I havent found a very detailed description about it.

1. argument: -id [0,100] maximum pairwise sequence identity (%) (def=90) Does this mean hhfilter will check identities between all protein sequence ? Or just comparison between protein sequence with first(seed) sequence ? And if two proteins are too similar, hhfilter will remove one of them? But how does hhfilter decide which one to remove? Short sequence?

2.argument: -cov [0,100] minimum coverage with query (%) (def=0)
May I ask what does "coverage" represent here ? Is it something similar with "coverage" in BLAST?

Thanks a lot for your time. I would be great to hear from you.

Best, Tao