From CAGT

Mutation Master Documentation

This program takes a multiple alignment file in MSF format.It is assumed that there may be partial sequences in the file.

The following actions are performed:

1. Splits the alignment into consecutive columns.
2. Calculates the number of sequences in a column. Note that for partial sequences, their participation in a column only counts in those columns that fall between the first and last letter of the partial sequence.
3. Calculates the number of different characters and their percentages of occurrence in each column. Same as above for partial sequences.
4. Plots the number of characters in a column.
5. Plots the percentages as stacked bars.
6. Makes a historgram of the number of columns with 1,2,3,... amino acids.
7. Provides a color plot showing the similarity of the amino acids to the consensus. Similarity is based on a substitution matrix. Numbers on the horizontal represent thecolumn. Column 1 is the leftmost column in the sequence.This graph is returned in .gif file format.