RIND: Reconstructed Independence
RIND: Reconstructed IndependenceGiven an alignment of protein sequences, 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.
For a more complete description of rind, see W.J. Bruno, "Modeling Residue Usage in Aligned Protein Sequences via Maximum Likelihood", Mol. Biol. Evol. 13:1368 (1996) (abstract) (BibTeX entry). Contact the author if you want to be on the mailing list.
| Source code | FTP access to the C program plus documentation and instructions. The code is intended for use in a UNIX environment with the PHYLIP package installed, but will run in other environments as well. |
| How To Use | Brief run-down on how you will execute the program once you download and compile it. |
| Examples | Text file describing some examples. |
| Thanks | Acknowledgments. |
| Bill Bruno's Home Page |