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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? |
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Replies: 2 comments 1 reply
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You could either do more iterations (e.g. -nm 10000) or you could do a standard (not ultrafast) bootstrap (e.g. |
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Sorry - logged in with wrong github account, this is actually @roblanf |
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Thank you! |
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You could either do more iterations (e.g. -nm 10000) or you could do a standard (not ultrafast) bootstrap (e.g.
-b 100would do 100 standard bootstraps, giving you estimates to the nearest ~1%).