Better to use smaller alignment reference areas?

[whitedavidp]

Here is my current setup:

The alignment step of the flow takes a long time, I feel. I am sure that it is always going to be the longest phase. But I wonder if I am making it take longer than is needed...

I see here under 1.2, mention of Alignment Search Field X + Y. In the popup help for these I read "...the search field should be as small as possible. The calculation time goes quadratic with the search field size." Mine is set to the default of 20 x 20.

But I wonder if the size of the alignment markers I specify in the web UI has any impact on this as well. I will try some empirical testing. But I may make poor conclusions. Any comments? Thanks

[whitedavidp]

In my early empirical testing, I would have to say that it appears that the alignment phase takes less time with smaller alignment references. Whether this impacts readings is yet unclear to me.