Based on that documentation :
And in particular, this command:
The nice thing about rapid bootstrapping is that it allows you to do a complete analysis (ML search + Bootstrapping) in one single step by typing raxmlHPC -f a -m GTRGAMMA -p 12345 -x 12345 -# 100 -s dna.phy -n T20 If called like this RAxML will do 100 rapid Bootstrap searches, 20 ML searches and return the best ML tree with support values to you via one single program call.
1) I always thought that Bootstrap searches and ML searches was the same. So what is the difference ?
2) -# 100 means 100 bootstrap but from where the 20 ML searches come from ?
3) Usually should we not set the same value for these 2 ?
Thanks for your help