HKY paralog analysis

These examples are taken from the analysis of variants of HKY models of nucleotide evolution of paralogous genes, possibly with some extra parameters or with some extra constraints.

• primate HKY+geneconv with tau=0
• yeast HKY+geneconv with tau=0
  • EM-like initialization plus quasi-Newton
  • EM for edge lengths only
• HKY+IGC free tau
  • finite differences gradient
  • explicit edge rate derivatives
• edge-specific posterior estimates
• PAML primate HKY85
  • Newick tree
  • Fasta file
  • Baseml control file
  • Output file (mlb)