Hi, I noticed that the valid values for fix_blength in Codeml.pm do not include option "fix_blength 1: initial", I agreed, I would add it myself in cvs: bioperl-run/Bio/Tools/Run/Phylo/PAML/Codeml.pm 'fix_blength' => [0,-1,2], change to: 'fix_blength' => [0,-1,1,2], Jason? Bests, Albert.