Rind computes a maximum-likelihood estimate of the number of times each residue was replaced into each position. Rind averages over several of the most likely phylogenies it is able to find using a user-specified distance-based method such as neighbor joining. The program can also make local changes to the topology when these will improve the likelihood. The evolutionary model used throughout the computation allows for different residue frequencies in each position, but ignores the genetic code.
- C Complier
:: MORE INFORMATION
“Modeling Residue Usage in Aligned Protein Sequences via Maximum Likelihood“,
Mol. Biol. Evol. 13:1368 (1996)