Proteinortho - Orthology detection tool
2014-03-05: Proteinortho V5.05 - Source code
2014-02-12: Proteinortho V5.04 - Source code
- Fixed stalling issues for system calls; these could have prevented Proteinortho from finishing an analysis at all
- Added -blastParameters option to define specific blast parameters other than E-Value
- Added -clean switch, it removes temporary files automatically
- Fixed some typos
- Eased thread locking and terminating system
- Added presort of blast results to speed up filtering
- Proteinortho now also parses options when set via --
2014-01-31: Proteinortho V5.03 - Source code (BETA)
- Fixed bugs in the selfblast implementation - Selfblast results obtained using V5.02 or V5.03 (BETA) should be reverified with this version!
- -singles option will add data on singleton genes directly into the results matrix rather than to a separate file
- Added tool to compare graph files (comp_bla.pl)
2014-01-27: Proteinortho V5.02 - Source code
- Added -singles option to return singleton genes (orphans without any matches)
- Improved multithreading: If more CPUs are present than required for blast jobs, blast's internal subthreads will be invoked
- Improved output: When already present blast output was found, a note is raised to give feedback to the user
2013-12-17: Proteinortho V5.0 - Source code
- Added -selfblast option to improve prediction of paralogs
2012-06-05: Proteinortho V4.26 - Source code
- PoFF extension added, which allows to incorporate conserved synteny data (-synteny, requires .gff files for gene positions)
- Default E-value changed from 1e-10 to 1e-05
- Partially reimplemented, more clear variable names and three step model (check/prepare, blast, cluster)
- Changed parameter names (run without options to see manual)
- Pairs will always be reported
- Tree-like structures in the orthology graph are not pruned anymore
2012-05-01: Proteinortho V4.25 - Source code
- Added -singles option, it allows to report single and paralogous genes found in one species only
2011-08-16: Proteinortho V4.22 - Source code
- Compatibility with newer blast+ v2.2.25
- Compatibility with newer versions of gcc
- Reduced default I/O-threads limit to 3
- Some details for better looking output
2011-01-12: Proteinortho V4.20 - Source code
- Added option to output the edge list for reciprocal blast alignments
- Added script to output the remaining edge list after clustering
- Added test+ option for make to run a test using blastp+ rather than blast+
- Relaxed criteria for compilation test to deal with different versions of blast
2010-12-17: Proteinortho V4.18 - Source code
- Support for NCBI blast+
- minor bugfixes
Proteinortho predicts (co-)orthologous proteins within different species.
The program was optimized for multi-core processors and low memory usage.
If necessary, Proteinortho allows to handle large sets with millions of proteins.
Several options for distributed computing on managed and unmanaged clusters are available.
Lechner et al (2011). Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinformatics 2011 Apr 28;12(1):124.
Proteinortho4 - Orthology detection tool
Po2Tree - Protein inclusion tree