All-by-all alignment issue

[daniel-dpq]

I did an all-by-all alignment against my own database with the default setting. From my understanding, if there exists an alignment between query A and target B, an alignment between query B and query A should also exist. But in many cases this is not true. Any reasons for this or should I change some settings?

Thanks for any help.

[martin-steinegger]

Our scores are not symmetrical since our bias corrections are query structure dependent.