This is an output example of the command qod --help:
******************************************************************************* * * * The QOD project aims to compare multiple genomes. * * qod version 1.0.2 * * * * Copyright © 2009-2012 -- LIRMM/CNRS * * (Laboratoire d'Informatique, de Robotique et de * * Microélectronique de Montpellier / * * Centre National de la Recherche Scientifique). * * * * Auteurs/Authors: The QOD Project <qod-project@lirmm.fr> * * Alban MANCHERON <alban.mancheron@lirmm.fr> * * Eric RIVALS <eric.rivals@lirmm.fr> * * Raluca URICARU <raluca.uricaru@lirmm.fr> * * * * Utilisez l'option '--full-version' pour de plus amples details. * * Run with the '--full-version' option for more details. * * * ******************************************************************************* usage: qod [Options] <files...> Mandatory arguments to long options are mandatory for short options too. Options must appears in the order of their description below. --help|-h Display this help and exit. --full-version|-V Display complete version header. --verbose|-v Display additional informations. --quiet|-q Turn off warnings. --tabular|-t Tabularize the output. --axt|-x Use this if input alignment files follow the AXT format. --ref-seq|-f <file> Set the central genome sequence from file <file> (fasta --eventually gzipped-- formatted). --annotations|-a <file> Read annotation of the central genome in file <file> (sequin --eventually gzipped-- formatted). <files...> The <files...> should contain the description of pairwise local similarities. Each file should contain the pairwise local similarities between the central genome and a given related genome. The files can be gzipped and must either follow the AXT format (if option --axt is provided) or formatted as follow: #Header #W_1 [a_1,b_1] [c_1,d_1] ... #W_n [a_n,b_n] [c_n,d_n] where W_i is the weight of the i^th interval, beginning at position a_i and ending at position b_i on the central genome sequence, and matching segment beginning at position min(c_i, d_i) and ending at position max(c_i,d_i) on the compared genome sequence. If c_i is greater than d_i, then the match occurs on the reverse complement of the compared sequence.