NOTES REGARDING SOFTWARE

NAME        Homo

VERSION     2.1

COPYRIGHT   Copyright © 2019-2023 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        4 November 2019

UPDATE      19 February 2023

PURPOSE     Homo conducts the matched-pairs test of symmetry for pairs of sequences of
            nucleotides, di-nucleotides, codons, genotypes and amino acids.
            
            Homo also computes three types of compositional distances between these pairs
            of sequences (including a compositional distance and the Euclidean distance)
 
FORMAT      Sequences must be stored in the FASTA format.
 
DATA TYPES  Sequences can be read as strings of singles, pairs or triplets of nucleotides, 
            as strings of 10- or 14-state genotypes, or as strings of amino acids.

COMPILE     g++ homo_v2.1.cpp -o homo -O3 -Wall -lm

HELP        Simply type homo in the command line

STATUS      Software complete

NOTE        Contact author for updates, etc

CITATION    Jermiin L.S., Jayaswal V., Robinson J. 2022. On making sense of multiple P 
            values from matched-pairs tests of homogeneity for pairs of homologous 
            sequences. Systematic Biology (in review).