Skip to content

Conversation

@trongnhanuit
Copy link
Member

  1. Set starting_rho = 0.5; converged = false;

  2. Run a loop with up to 10 iterations
    1.1. Optimise rho from starting_rho and cbl from current branch length (of non-fundi model) to obtain fundi log-likelihood.
    1.2. If the resulting log-likelihood is not lower than non-fundi: converged = true; Stop.
    1.3. Reduce the starting_rho by half (i.e. 0.25 in the first iteration, 0.125 in the 2nd iteration, so on). Go back to step 1.1.

  3. If not converged -> reset rho = 0 (non-Fundi model)

Copy link
Member

@bqminh bqminh left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

all good, thanks Nhan!

@bqminh bqminh merged commit c5c5c0a into iqtree:master Dec 20, 2025
6 of 8 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants