0. Prerequisites

ADOPS needs T-Coffee, MrBayes and CodeML applications in order to work, so you will have to install them before start with this installation process.

You can find the installation files and instructions of this programs in their respective web pages:

1. Download

Download your ADOPS copy from here (9.5MB) and go to step 2.
Or you can download this Ubuntu 14.04 (64 bits) Virtual Machine (~1.6GB) with a copy of ADOPS, T-Coffee, MrBayes and PAML already installed and configured (also the BDBM software). Run the virtual machine (you will need Virtual Box) and go to step 4.

If you have some trouble installing the ADOPS VM, you can check our ADOPS VM - Quick Installation Guide.

2. Decompress

ADOPS directory structure
Figure 1. ADOPS file structure

Decompress the downloaded file (you will need a ZIP decompressor).

You can decompress and install ADOPS in any folder, although we recommend you to install it in a folder without spaces in its path due to some problems with the programs used by ADOPS. For example:

  • /home/user/ADOPS [OK]
  • C:\Programs\ADOPS [OK]
  • /home/user/My Programs/ADOPS [Not recommended]
  • C:\Documents and settings\ADOPS [Not recommended]

Once decompressed you should have a directory structure like seen in Figure 1.

3. Configure

Before start working with ADOPS you have to configure the paths to MrBayes and CodeML applications.

Open the system.conf configuration file and set the appropriate value to the following properties:

tcoffee.bin
T-Coffee command. T-Coffee must be in the system path1
mrbayes.dir
Path to the MrBayes installation directory. Independently of your OS use / as path separator (e.g. C:/Users/john/mrbayes/) [Required]
mrbayes.bin
Name of the MrBayes executable file
codeml.dir
Path to the CodeML installation directory. Independently of your OS use / as path separator (e.g. C:/Users/john/paml/) [Required]
codeml.bin
Name of the CodeML executable file [Required]

System configuration file should look as follows:

input.sequences=
input.fasta=
input.names=

tcoffee.bin=<T-Coffee command>
tcoffee.params=
tcoffee.maxSeqs=3
tcoffee.alignMethod=CLUSTALW2

mrbayes.mpich=
mrbayes.dir=<Path to MrBayes>
mrbayes.bin=<MrBayes executable>
mrbayes.params=
mrbayes.ngen=500000
mrbayes.tburnin=1250
mrbayes.pburnin=1250

codeml.dir=<Path to CodeML>
codeml.bin=<CodeML executable>
codeml.params=
codeml.models=0 1 2 3 7 8

4. Launch!

Now you are ready to launch ADOPS.

In case you are under a Windows environment you have to execute the run.bat file. Otherwise, if you are under a Linux environment you have to execute the run.sh file.

If you want to test the application you can download this example files:

Note: Mac OS support comming soon...


Citing ADOPS

If you use ADOPS, please, cite this article:

D. Reboiro-Jato, M. Reboiro-Jato, F. Fdez-Riverola, C.P. Vieira, N.A. Fonseca, J. Vieira
ADOPS - Automatic Detection Of Positively Selected Sites
Journal of Integrative Bioinformatics, 9(3):200, 2012.
Online Journal: http://journal.imbio.de/index.php?paper_id=200

Works using ADOPS

These are some works that use ADOPS:

A.R. Araújo, M. Reis, H. Rocha, B. Aguiar, R. Morales-Hojas, S. Macedo-Ribeiro, N.A. Fonseca, D. Reboiro-Jato, M. Reboiro Jato, F. Fdez-Riverola, C.P. Vieira, J. Vieira
The Drosophila Melanogaster Methuselah Gene: A Novel Gene with Ancient Functions
PLOS ONE, 8(5):e63747, 2013.
Online Journal: http://dx.doi.org/10.1371/journal.pone.0063747

B. Aguiar, J. Vieira, A.E. Cunha, N.A. Fonseca, D. Reboiro-Jato, M. Reboiro-Jato, F. Fdez-Riverola, O. Raspé, C.P. Vieira
Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S-pollen genes support the 'non-self recognition by multiple factors' model
Journal of Experimental Botany, 64(8):2423-2434, 2013.
Online Journal: http://dx.doi.org/10.1093/jxb/ert098

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