psicalc 0.2.3

Algorithm for clustering protein multiple sequence alignments using normalized mutual information.

PSICalc Algorithm Package

This is a package for clustering Multiple Sequence Alignments (MSAs) utilizing normalized mutual information to examine protein subdomains. A complete data visualization tool for psicalc is available here: https://github.com/mandosoft/psi-calc.

As an example:

import psicalc as pc

file = "<your_fasta_file>" # e.g "PF02517_seed.txt"

data = pc.read_txt_file_format(file) # read Fasta file

data = pc.durston_schema(data, 1) # Label column index starting at 1

result = pc.find_clusters(7, data) # will sample every 7th column

pc.write_output_data(7, result)

The program will run and return a csv file with the strongest clusters found in the MSA provided.