biology/paml: Update to version 4.9j


biology/paml: Update to version 4.9j

  • Remove BROKEN=. Version 4.9i became unfetchable when the author pulled the tarball to prevent users from downloading a version with new, serious bugs.

Upstream changes described by the author:

  • mcmctree: Initial values have ages that are too old, exceeding max bounds. In theory bounds in mcmctree are always soft so that the node ages will move to the area of posterior mode when burnin is long enough. In practice the poor starting values are problematic and requires long burn-in. I have rewritten the code for generating initial values to respect the min and max bounds specified in the fossil calibrations.
  • codeml: A bug introduced in 4.9i caused the clade labels ($) to be ignored. This affects the branch, branch-site and clade models. If your tree has branch labels (#) only and no clade models, everything will be fine. If you have used the clade label ($) in the tree with or without the branch label (#), either the program will abort or the results will be incorrect. The clade label ($) is supposed to label all branches in the clade as well as the branch itself, but all clade labels in the tree are ignored in 4.9i. Earlier versions are correct.


jrmFri, Nov 22, 3:32 PM
rP518149: New ports required for gitlab-ce 12.5.