Download Ortholuge Software

The Ortholuge method is described in the paper Fulton DL, Li YY, Laird M, Horsman BGS, Roche FMR, Brinkman FSL. Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics, 2006. 7:270. Please cite this paper if you use Ortholuge. The Ortholuge software may be obtained from this site and used free of charge. It is distributed under the GNU General Public License (GNU GPL).

Compatibility

Ortholuge was developed using Perl under Linux (SuSE 9.0 and RH 9.0). Provided all the needed tools are available for your operating system it should work under any UNIX flavour.

Required programs

• Perl version 5.6.x or higher - The latest version of Perl can be obtained from http://www.cpan.org
• The Bioperl library version 1.4 or higher - While Ortholuge should work with Bioperl 1.2, 1.4 or above is highly recommended. Bioperl can be obtained from http://www.bioperl.org
• A working installation of standalone NCBI BLAST - BLAST can be obtained from ftp://ftp.ncbi.nih.gov/blast/executables/
• Either:
  • 1. MUSCLE multiple sequence alignment tool, version 3.52 or higher - MUSCLE can be obtained from http://phylogenomics.berkeley.edu/muscle/. MUSCLE 3.6 has been tested for combatability with the Ortholuge 0.8 package and we recommend you use this version. The MUSCLE 3.6 source code and linux binary are available here:
    • MUSCLE 3.6 Source Code muscle3.6_src.tar.gz
    • MUSCLE 3.6 Linux Binary muscle3.6_linux_ia32.tar.gz
    - OR -
  • 2. ClustalW multiple sequence alignment tool - ClustalW can be obtained from ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
• The PHYLIP package of the EMBASSY Program Suites from EMBOSS (version 3.57c or 3.6b) - PHYLIP can be obtained from http://www.hgmp.mrc.ac.uk/Software/EMBOSS/EMBASSY/. The EMBOSS 3.0.0 package and PHYLIP 3.6b EMBASSY application have been tested for combatability with the Ortholuge 0.8 package and we recommend you use these versions. The EMBOSS 3.0.0 and PHYLIP 3.6b source code is available here:
  • EMBOSS 3.0.0 EMBOSS-3.0.0.tar.gz
  • PHYLIP 3.6b PHYLIP-3.6b.tar.gz
• The Perl SVG 2.33 package - Perl SVG 2.33 can be found at http://search.cpan.org/~ronan/SVG-2.33/
• ImageMagick image conversion suite - Only required if you plan to output graphics in png format. Imagemagick can be found at http://www.imagemagick.org/

Ortholuge Executables

• ortholuge-0.8.edist.tar.gz (for Phylip 3.57c)
• ortholuge-0.8.fdist.tar.gz (for Phylip 3.6b)

Documentation

• README.txt
• INSTALL.txt
• CHANGES.txt
• Sample Configuration File

Disclaimer

THE DATA AND SOFTWARE ARE PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.

This project is supported by Genome British Columbia, Genome Prairie and Genome Canada, a not-for-profit organization which is leading Canada's national strategy on genomics with $ 600 million in funding from the federal government.