Proteinortho - Orthology detection tool - Past releases
Downloads
2016-08-26: Proteinortho V5.15 - Source code with precompiled binaries (Linux/x64) / Proteinortho V5.15 - Source code only
- output table is ordered by species names and gene names which largely increases readability and comparability
- increased arithmetic accuracy of graph clustering
- added warning before existing outputs are overwritten
- added support for tblastx+ and tblastx legacy
thanks to Clemens Thölken
2016-04-26: Proteinortho V5.13 - Source code
- fixed issue in graph clustering that sometimes led to random artefacts
thanks to David Kraus (MPI Marburg) and Andrey Rozenberg (University of Bochum)
- added hardening modifications for Makefile and added tree builder as install target
thanks to Andreas Tille
- Known issues: edges the cleaned graph file (proteinortho-graph) are not reliable at the moment (do not reflect in-program graph)
2016-03-17: Proteinortho V5.12b - Source code
- fixed Makefile (version b)
- fixed code issue in tree builder that prevented it from compiling (version b)
- fixed issue where clustering could take very long or even get stuck
- improved clustering accuracy for small graphs
- added feature to use user-defined temporary paths (-temp=[PATH])
- adapted and re-added UPGMA-tree builder tool for protein presence/absence from the version 4 branch (po2tree)
2014-09-23: Proteinortho V5.11 - Source code
- fixed bug when using -singles options with files subfolders
2014-07-26: Proteinortho V5.10 - Source code
- speeded up graph processing (a lot)
- improved make test and example files
- fixed minor bugs in tool and manual
- added some bugtracking output data to ease use
2014-07-01: Proteinortho V5.07 - Source code
- Added a more detailed manual
- Added example data for test
- Minor bugfixes in output data
2014-04-01: Proteinortho V5.06 - Source code
- Made graph output optional: now it needs to be requested using the -graph switch
- Added a new output file: XXX.descriptions containing ID DESC from FASTA files
- Fixed some typos and description flaws
- Tweaked Makefile
- Special thanks for this update goes to Torsten Seemann, Victorian Bioinformatics Consortium at Monash University, Clayton
2014-03-05: Proteinortho V5.05 - 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 --
2014-02-12: Proteinortho V5.04 - Source code
- 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)
2014-01-31: Proteinortho V5.03 - Source code (BETA)
- 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
2014-01-27: Proteinortho V5.02 - Source code
- Added -selfblast option to improve prediction of paralogs
2013-12-17: Proteinortho V5.0 - 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
2012-06-05: Proteinortho V4.26 - Source code
- Added -singles option, it allows to report single and paralogous genes found in one species only
2012-05-01: Proteinortho V4.25 - 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
2011-08-16: Proteinortho V4.22 - 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
2011-01-12: Proteinortho V4.20 - Source code
- Support for NCBI blast+
- minor bugfixes
2010-12-17: Proteinortho V4.18 - Source code
Description
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.
Citation
Lechner et al (2011). Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinformatics 2011 Apr 28;12(1):124.
Manuals
Proteinortho4 - Orthology detection tool
Po2Tree - Protein inclusion tree