It can also optionally determine and graph the information content for each individual position of the matrix. Matrices can be either horizontal or vertical. In a horizontal matrix, the columns correspond to the positions within the alignment, and the rows correspond to the letters. In a vertical matrix, the rows correspond to the positions within the alignment, and the columns correspond to the letters. The input files can contain comments according to the following convention.
Comments can begin anywhere in a line and always end at the end of the line.
The output of this program is sent to the standard output. The number of sequences in the alignment. This option is necessary only if no position of the alignment contains a representative from every sequence. This situation can only occur in alignments that ignore terminal gaps. Adjust the information by subtracting the indicated number of standard deviations expected from a random alignment from each position of the alignment.