Proteinortho - Orthology detection tool - Past releases

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• 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

• 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)

• 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)

• fixed bug when using -singles options with files subfolders

• 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

• Added a more detailed manual
• Added example data for test
• Minor bugfixes in output data

• 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

• 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 --

• 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)

• 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

• Added -selfblast option to improve prediction of paralogs

• 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

• Added -singles option, it allows to report single and paralogous genes found in one species only

• 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

• 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

• Support for NCBI blast+
• minor bugfixes

Description

Citation

Manuals