Proteinortho - Orthology detection tool
Proteinortho is a tool to detect orthologous genes within different species. This software can used, redistributed and modified GNU General Public License version 2 or later.
The project is now made available via GitLab.
Latest Proteinortho6 version (GitLab)
If you use Proteinortho in your work you might want to cite:
Lechner et al (2011). Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinformatics 2011 Apr 28;12(1):124.
View Proteinortho6 / PoFF manual
2019-02-05: Proteinortho V6.0b - Source code
View Proteinortho5 / PoFF manual
2017-09-22: Proteinortho V5.16b - Source code with precompiled binaries (Linux/x64) / Proteinortho V5.16b - Source code only
- speedup in similarity search: replaced blastp with diamond (blast is still available)
- speedup in clustering: weighted clustering, multi-core support, LAPACK implemention
- solved issues when clustering of huge connected components took very long
- automatic detection of NCBI-style GFFs for synteny extension
2017-04-18: Proteinortho V5.16 - Source code with precompiled binaries (Linux/x64) / Proteinortho V5.16 - Source code only
terminate called after throwing an instance of 'char const*' error
Past releases can be found here
- simplified distribution of jobs for multiple PCs/nodes, -startat and -stopat were exchanged by -jobs=N/M (!)
- solved reproducibility issues due to symmetric graph structures (see option -purity)
- same gene ids can now be used in different species at the same time
- occurrence of the same gene id within a single species is reliably detected
- fixed issues when using the -selfblast option
- detection of available CPUs is more robust
- compatibility to GFF3 files generated by prokka
thanks to Ben Woodcroft
- Known issue:
The clustering step might return
terminate called after throwing an instance of 'char const*'.