MetaxaQR: Accurate classification and curation of current and future DNA barcodes
Version: 3.0 b3 NOTE THAT THIS IS A BETA VERSION OF METAXAQR!
Copyright (C) 2011-2024 Johan Bengtsson-Palme et al.
Contact: Johan Bengtsson-Palme, johan.bengtsson-palme[at]microbiology.se
A very quick installation guide follows below.
MetaxaQR requires Perl, Python, HMMER3, Vsearch and MAFFT to function properly. Python is required for the MetaxaQR Database builder.
1) Perl and Python usually installed on Unix-like systems by default. If not, it can be retrieved from http://www.perl.org/ and https://www.python.org/
2) HMMER3 can be found at http://hmmer.org/download.html Download it and follow the on site instructions for installation.
3) Vsearch can be downloaded from https://github.com/torognes/vsearch Download it and follow the on site instructions for installation. Make sure to use a vsearch version >2.5.1 for MetaxaQR compatibility.
4) MAFFT can be obtained from http://mafft.cbrc.jp/alignment/software/ Download the package for your operating system, and follow the installation instructions on the download page. If you do not have admin privileges on your machine, take a look at these instructions: http://mafft.cbrc.jp/alignment/software/installation_without_root.html
5) Obtain the MetaxaQR package from https://github.com/bengtssonpalme/MetaxaQR/ Unpack the package (if needed) and move it to your desired directory.
6) Install MetaxaQR by running the script ./install_metaxaQR (or alternatively by copying all the files beginning with "metaxaQR", the "metaxaQR_dbb" and "src" directories and the file "get_fasta" into your preferred bin directory)
7) To test if MetaxaQR was successfully installed type "metaxaQR --help" on the command-line. You should now see the MetaxaQR help message.
8) Download the SSU database from the MetaxaQR Database Repository to get started:
metaxaQR_install_database -g SSU
To run MetaxaQR, you need a FASTA-formatted input file. To check for SSU rRNA sequences in a FASTA file, type metaxaQR -i file.fasta -o test -g SSU on the command line. If you are on a multicore machine, you might want to use the --cpu 2 option to speed up the processes by using two (or more) cores.
If you encounter a bug or some other strange behaviour, please report it to: metaxa[at]microbiology.se
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, in a file called 'license.txt'. If not, see: http://www.gnu.org/licenses/.