Package: aaMI
Version: 1.0-1
Date: 2005-07-08
Title: Mutual information for protein sequence alignments
Author: Kurt Wollenberg <kurt.wollenberg@gmail.com>
Maintainer: Kurt Wollenberg <kurt.wollenberg@gmail.com>
Depends: R (>= 2.0.0)
Description: This package contains five functions. read.FASTA reads in a 
     FASTA-format alignment file and parses it into a data frame. read.CX reads 
     in a ClustalX .aln-format file and parses it into a data frame. read.Gdoc 
     reads in a GeneDoc .msf-format file and parses it into a data frame. The 
     alignment data frame returned by each of these functions has the sequence 
     IDs as the row names and each site in the alignment is a column in the data 
     frame. The program aaMI calculates the mutual information between each pair 
     of sites (columns) in the protein sequence alignment data frame. The 
     program aaMIn calculates the normalized mutual information between pairs of 
     sites in the protein sequence alignment data frame. The normalized mutual 
     information of sites i and j is the mutual information of these sites 
     divided by their joint entropy.
License: GPL version 2 or newer
Packaged: Mon Oct 17 11:06:36 2005; kwollenberg
