Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models

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Orthograph was published in BMC Bioinformatics (2017). Please cite this paper when you use Orthograph for your academic publications.


A manual page containing a description of all options is in the doc directory. It can be read using man -l doc/orthograph.man or directly with man orthograph if installed properly (ask your system administrator). You can also generate a pretty PostScript version using man -Tps -l doc/orthograph.man > doc/manual.ps. Most PDF viewers also accept PostScript files.

For quickstart instructions, read the supplied README.md file (it's a text file, so just open it with any text editor/viewer).


Orthograph requires the following software packages to be installed on the system. The whole package was tested and works with these versions, and newer versions should be no problem. Downwards compatibility (i.e., older versions) has not been tested. Should be fine, too, but be wary with MAFFT, its developers change or drop features frequently across versions. Also, there has been a report about an older SQLite version not working, so make sure you have a reasonably recent one.

You only need SWIPE if you want to use it.

You need a database backend, either SQLite (the default) or MySQL. If you don't know which one to pick, use SQLite. It's easier to install and use, but doesn't have the capabilities for a centralized server-client setup. In grid computing environments, this is an advantage since no network connections are required, but the database is a flat file on the hard drive.

Package Version Download from
Perl 5.14 http://www.perl.org
SQLite 3.8.2 http://sqlite.org/download.html
MySQL 5.6.17 http://dev.mysql.com/downloads/mysql/
MAFFT 7.273 http://mafft.cbrc.jp/alignment/software/
HMMer 3.1b1 http://hmmer.janelia.org
NCBI BLAST+ 2.2.28+ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Exonerate 2.2.0 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
SWIPE 2.0.12 https://github.com/torognes/swipe

Make sure you get the correct versions for your operating system (most packages are provided as 32 bit and 64 bit versions).

If you use some flavor of Linux, these packages are most likely present in your software repositories. It is recommended to install them using apt-get, yum, or whatever package manager your system uses. Additionally, you need the Perl modules DBI or DBD::mysql or DBD::SQLite, depending on your database choice.

Don't worry about your Perl version if you run a reasonably recent Linux or UNIX system, such as Mac OS X, but see here and there if you are trying to install the required packages on a Windows system under Cygwin (or natively, for that matter). You might run into problems getting the MySQL driver, HMMer3 and Exonerate to work. Really, don't use Windows.

Make sure you have the database interface module DBI for your Perl version as well as the proper database driver for your database engine of choice (DBD::mysql or DBD::SQLite)

If you get an error like "Can't locate Some/Module.pm in @INC", you need to update your Perl installation.


Please see the supplied README file for further instructions on how to set up and run Orthograph.