DOMINO is a new software application specifically designed for improving the development of DNA markers in non-model organisms using either NGS data or pre-computed multiple sequence alignments (MSA) in various formats (including RAD loci). It uses Perl and C++ scripting languages to combine some popular, open-source, bioinformatics tools for NGS data with a set of new developed functions in an integrated bioinformatics pipeline for custom-made marker discovery or selection based on user-defined criteria.
Customizable features include the length of variable and conserved regions (when requested), the minimum levels (or a preferred range) of nucleotide variation, how to manage polymorphic variants, or which taxa (or what fraction of them) should be covered by the marker. All these criteria can be easily defined in a user-friendly GUI or under a command-line version that implements some extended options and that it is particularly useful for working with large NGS data sets in high performance computers (see also the DOMINO documentation). The regions identified or selected in DOMINO can be i) directly used as markers with a particular depth of taxonomic resolution, ii) utilized for their downstream PCR amplification in a broader taxonomic scope or iii) used as suitable templates to optimized bait design for target DNA enrichment techniques.
Documentation and additional information can be retrieved from the DOMINO oficial website: http://www.ub.edu/softevol/domino/
DOMINO is developed and maintained under GNU/Unix using ANSI/ISO C and standard development tools (GCC, Autotools).
It can be compiled and run in Linux (Ubuntu 14.04 LTS) and Mac OSX systems (version > 10.10)
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Perl Programming Language version v5.2+
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C++ compiler
- Mac OS users may need to install Xcode package via App Store
- Linux users may need to install build essential package o g++ compiler Ubuntu: sudo apt-get install build-essential or sudo apt-get install g++
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zlib compression library v1.2.3+ (SAMtools dependency) http://www.zlib.net/
- Mac OS: included and installed in the distribution.
- Linux users may need to install zlib1g-dev package Ubuntu/Linux Mint: sudo apt-get install zlib1g-dev
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Xterm (in some ubuntu-like distributions may not be included):
- Mac OS: included and installed in the distribution
- Ubuntu/Linux Mint: sudo apt-get install xterm
Two possible installation options:
In the DOMINO website, user can obtain installers that will guide the user through the complete installation process for Linux and Mac distributions.
Also, all the necessary installation files and folders (the user may need to compile and retrieve some Qt libraries) are available at the domino Git repository.
Once installed, the bin directory will contain the DOMINO perl scripts, the directories with the binaries of the external software included in the DOMINO pipeline and some mandatory Perl modules. In addition, a shortcut Desktop DOMINO icon will be generated.
In the Git directory, the user can find a pre-configured shell script (install.sh) written to handle the installation of command-line version (to install only the command-line version).
In a Unix-based bash console, change the directory to enter in the desired installation folder and run the script, with the command: sh install.sh
The bin directory will contain the DOMINO perl scripts, the directories with the binaries of the external software included in the DOMINO pipeline and some mandatory Perl modules.
If you encounter bugs that are not listed here, please send comments and bug reports via GitHub
ATTENTION:
We have very limited funds for the maintenance of this software. Therefore we can not garantee a full support. Moreover, we are also working in the development of a new implementation of DOMINO (including other features). We will announce it through this (and other) channels.
If you would like to see a new feature implemented, suggestions are welcome. Our aim is to have a "suggestion" box soon.
The authors would like to thank all people who contributed (and are still contributing) in the creation and testing of this software.
Cristina Frias-Lopez, Jose F. Sanchez-Herrero, Miquel A. Arnedo, Alejandro Sanchez-Gracia and Julio Rozas.
C.Frias-Lopez: [email protected]
J.F.Sanchez-Herrero: [email protected]
M.A. Arnedo: [email protected]
A.Sanchez-Gracia: [email protected]
J.Rozas: [email protected]
Evolutionary Genomics and Bioinformatics Group, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona 08028, Spain
Cristina Frías-López, José F. Sánchez-Herrero, Sara Guirao-Rico, Elisa Mora, Miquel A. Arnedo, Alejandro Sánchez-Gracia, Julio Rozas, DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3753–3759, https://doi.org/10.1093/bioinformatics/btw534
Copyright (C) 2016 Evolutionary Genomics and Bioinformatics Group, University of Barcelona.
DOMINO is licensed under the GPLv3 license. See `LICENSE' file for details.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/