Mutual information for protein sequence alignments
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.