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Automatic Detection of Positively Selected Sites
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README.md

ADOPS

ADOPS (Automatic Detection Of Positively Selected Sites) software was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data.

Team

Molecular Evolution Group - IBMC:

  • Jorge Vieira
  • Cristina P. Vieira
  • Nuno A. Fonseca

SING Group - Universidade de Vigo:

  • Miguel Reboiro-Jato
  • David Reboiro Jato
  • Florentino Fdez-Riverola
  • Noé Vázquez González
  • Hugo López-Fernández

Downloading and Installing ADOPS

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 12.04 (32 bits) Virtual Machine (~2GB) with a copy of ADOPS, T-Coffee, MrBayes and PAML already installed and configured. 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

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:

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

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]

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:

Citing ADOPS

If you use ADOPS, please, cite this work:

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.


1 Unfortunately, there is no Windows 64 bits version of T-Coffee, so you will need a MacOS, Linux or Windows 32 bits system.

2 Data set taken from Expression and Trans-Specific Polymorphism of Self-Incompatibility RNases in Coffea (Rubiaceae). Nowak, M., Davis, A., Anthony, F., Yoder, A. PloS one 6(6) (2011)

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