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:
- Splits the alignment into consecutive columns.
- 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.
- Calculates the number of different characters and their percentages of occurrence in each column. Same as above for partial sequences.
- Plots the number of characters in a column.
- Plots the percentages as stacked bars.
- Makes a historgram of the number of columns with 1,2,3,... amino acids.
- 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.