Full alignment or polymorphic sites only? about modeltest HOT 3 OPEN

Hi "apredeus",

I think it is better to use the whole alignment, unless if you don't care about the branch lengths and model parameters. You should not observe a significant difference in computational time or memory requirements, because those 20k sites will be actually compressed into just 4, having their corresponding weights.

Best,
Diego

from modeltest.

Thank you very much for your reply. The analysis was taking days, so I wasn't sure if I was doing something wrong.

from modeltest.

Definitely with such a large number of taxa it can take several days of analysis, particularly if you are doing a sequential analysis. Which run arguments are you using?

from modeltest.