suggestion for bootstrap

[txuemei]

Got the warning "bootstrap analysis did not converge" in IQ-TREE which suggests that the number of bootstrap replicates may not have been sufficient for convergence. Even though I set -B 1000 (for ultrafast bootstrap) and -nm 2000 (for bootstrap stopping criteria), the analysis still did not reach a stable support value. What I should do?

[DS4B-ANU]

You could either do more iterations (e.g. -nm 10000) or you could do a standard (not ultrafast) bootstrap (e.g. -b 100 would do 100 standard bootstraps, giving you estimates to the nearest ~1%).

[DS4B-ANU]

Sorry - logged in with wrong github account, this is actually @roblanf

[txuemei]

Thank you!