NOTES REGARDING SOFTWARE

NAME        RandAlign

VERSION     1.0

COPYRIGHT   Copyright © 2019-2022 Lars Sommer Jermiin. All rights reserved.

WARNING     The copyright holder takes no legal responsibility for the correctness of 
            results obtained using this program.

AUTHOR      Lars Sommer Jermiin

ADDRESS     Australian National University
            University College Dublin            

CONTACT     lars.jermiin@anu.edu.au
            lars.jermiin@ucd.ie

DATE        13 June 2022

PURPOSE     RandAlign reads a multiple sequence alignment, shuffles the content across:

              1. sites within each sequence [retains entropy of each sequence];
              2. sequences within each site [retains entropy of each site];
              3. sites as well as sequences.
              
            All sites or variant sites are considered.

            The resulting alignments are printed to two files.
 
FORMAT      Sequences must be stored in the FASTA format.
 
DATA TYPES  Nucleotides, di-nucleotides, codons, 10-state genotypes, 14-state genotypes 
            and amino acids.

COMPILE     g++ randalign.cpp -o randalign -O3 -Wall

HELP        Simply type randalign in the command line

STATUS      Software complete

NOTE        Contact author for updates, etc