aaMI

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.