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.

Downloads

The project is now made available via GitLab.

Manual

Manual (README.md)

Current version

Latest Proteinortho6 version (GitLab)

Citation

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.

Old versions

View Proteinortho6 / PoFF manual 2019-02-05: Proteinortho V6.0b - Source code

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

View Proteinortho5 / PoFF manual 2017-09-22: Proteinortho V5.16b - Source code with precompiled binaries (Linux/x64) / Proteinortho V5.16b - Source code only

solved terminate called after throwing an instance of 'char const*' error

2017-04-18: Proteinortho V5.16 - Source code with precompiled binaries (Linux/x64) / Proteinortho V5.16 - Source code only

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*'.

Past releases can be found here