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
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
06-05: Proteinortho V4.26 - Source code
Added -singles option, it allows to report single and paralogous genes found in one species only
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
2014
01-27: Proteinortho V5.02 - Source code
Added -selfblast option to improve prediction of paralogs
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
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)
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 --
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
07-01: Proteinortho V5.07 - Source code
Added a more detailed manual
Added example data for test
Minor bugfixes in output data
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
09-23: Proteinortho V5.11 - Source code
fixed bug when using -singles options with files subfolders
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)
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)
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
2018 Proteinortho6
20.Juni-4.Juli
openmp support (max_of_diag,get_new_x,makeOrthogonal,normalize,getY)
bitscore integration in the convergence (weighted algebraic connectivity)
protein output is now sorted in descending degree-order (sort with comparator_pairDoubleUInt)
getConnectivity: special case checks now if the induced subgraph is complete (K_n)
added various test functions
5. Juli
added kmere heuristic for splitting groups in proteinortho_clustering. After the calculation of an fiedler vector, the kmere heuristic splits the graph not only in the positive and negative entries of the vector but in k clusters. k=2 -> the original split (without the purity).
16. Juli
added LAPACK support for CC with less than 2^15 nodes (since it uses quadratic space -> (2^15)^2=2^30) for the calculation of the algebraic connectivity.
added all other proteinortho files to this repository.
graphMinusRemoveGraph.cpp implements proteinortho5_clean_edges2.pl in c++
23.Juli
openMP support for laplacian declaration (for lapack).
'make test' clean up.
jackhmmer, phmmer, diamond, usearch support.
24 Juli
last integration.
phmmer+jackhmmer fix/workaround (there is no local identity in the output -> disabled).
proteinortho.pl : set cluster algorithm to weighted-mode as default.
30. Juli
rapsearch integration.
proteinortho_clustering.cpp : -ramLapack is now -ram and is the threshold for laplace matrix + graph struct.
added dynamic memory management (proteinortho.pl + clustering.cpp) using the free -m command (if exists)
31. Juli
rapsearch fix (wrong order of db and q)
purity is back, now 0.1 (and fallback function, if all nodes are below purity threshold -> remove purity for this connected component)
more options for proteinortho.pl -p=diamond-moresensitive|usearch-ublast
9. Aug
topaz integeration.
all DBs now have the blastmode in name (colliding names) as well as the tmp files generated by the blastalgos.
10. Aug
Orthology XML integration. Added the option -noxml for not generating the orthology XML format.
13. Aug
bugfix usearch/ublast: removed the description from the gene name (formatU.pl). bugfix rapsearch: forced to create an output .m8 file if there are no hits found.
allowedAlphabet check in read_details in check_files. E.g. diamond expects aminoacid characters -> found a gene with only nucleotide characters -> WARNING. E.g. blastn+ expects nucleotide characters -> found non nucleotide characters -> ERROR.
22. Aug
removed phmmer and jackhmmer.
removed the -p=diamondmoresensitive option, since it is equivalent to -p=diamond -subpara='--moresensitive'.
# redesigned the multithreading system:
# -cpus=x -> spawn round(sqrt(x)) workerthreads with each ceil(sqrt(x)) (different for the last workerthread ...) cores for blast.
# removed threads_per_process function.
8. Sep
proteinortho_clustering: introduced multithreading in partition_graph() -> generate k CC and compute the lapack dsyevx in parallel (1. Memory check 2. if a large CC is found -> 1 power iteration with all cores 3. else do k lapack.). New const variable lapack_power_threshold_n for determining large CC for the power iteration.
4. Okt
improvement in the memory calculations.
BUGfix in the DFS calculation (recursion in c++ failed with segmentation fault if the recursion was too deep) -> now iteratively (memory ineffciently) with Queue
10. Okt
DFS -> BFS since recursive calls can only be so deep.
18. Okt
purity is now 1e-7, evalue 1e-8 (http://people.sc.fsu.edu/~jburkardt/c_src/power_method/power_method_prb.c)
kmere heuristic minNodes = 2^20 (~1e+6), kmere now checks if the "normal" split would result in a good partition.
30. Okt
- removed the memory manager for proteinortho_clustering, instead a simple n threshold manages the power/lapack algorithms
now all CC are calculated for power/lapack (no frequent restart), dynamic for loop for lapack
7. Nov
dsyevr instead of dsyevx (rrr algorithm now)
remove graph bugfix (each thread is now assigned an own ofstream (shared_ptr needed -> c++11 needed))
13. Nov
OMP_PROC_BIND=close for multi-socket systems (change the cpu affinity of openmp to close -> each new thread spawn next to the last one, instead of randomly)
15. Nov
Blat support (step=2), the evalues cannot be preset as a parameter but appear if -out=blast8 is set.
16. Nov
proteinoprtho 6.0 alpha release
28. Nov
Makefile update (lapack zipped,...)
5. Dez
MCL integration (-mcl option in proteinortho.pl)
XML bugfix (species with . in the name did confuse the xml parser)
6. Dez
MCL pre/postprocessing (src/do_mcl.pl)
double -> float in proteinortho_clustering.cpp
weights are unsigned shorts again (only the last commit was unsigned int) proteinortho_clustering.cpp
10. Dez
gff4fasta update: Test for additional naming schemes
orthoXML improvement (still not accepted by orthobechmarkproject)
25. Dez
no lapack version (src/proteinortho_clustering_nolapack.cpp)
no cmake version (make all_nocmake, needs lapack installed)
2019
9. Jan
pow_n replaced with powLapD (graph density threshold instead of number of nodes)
11. Jan
mmseq2 integration (proteinortho.pl) -p=mmseqsp or mmseqsn
22. Jan (uid:296)
Added CHAGEUID for a commit specific id. (update_CHANGEUID.sh can be found in snippets, use 'find . -maxdepth 2 | perl -lne '{if($_=~m/^.*(\.pl|\.cpp|\.c|\.h|\.md|\.txt|Makefile|CHANGELOG)$/){print $_;}}' | entr bash update_CHANGEUID.sh')
BUGfix: weird sort behaviour dependant on locale (LC_All,LC_NUMERIC). Fix: $ENV{'LC_All'}='C';
23. Jan (uid:492) v6.0a
small fix for get_po_path
4. Feb (uid:724)
-ram is back for memory control of proteinortho_clustering (restricts the memory usage of LAPACK and the input graph), works also for proteinortho.pl -ram
14. Mar (uid: 1034)
-tmp is now working better (tmp_dir now generates a directory with all temporary files inside)
read_details now checks if the input files are faa and fna type based on the -p algorithm (diamond only uses faa files etcpp) IF -checkfasta
20. Mar (uid: 1174)
static versions (Linux/x64) of all binaries are now included in the repository
Makefile now compiles first against /usr/lib/liblapack statically then it tries to recompile src/lapack automatically with 'make'
26. Apr (uid: 2239)
now supports -minspecies fully (proteinortho.pl argument)
fix no_lapack_proteinortho_clustering
po2html integration
28. Apr (uid:2349)
Makefile now builds in src/BUILDS/$uname depending on the system (Linux/Darvin). Now I can include precompiled binaries for mac and linus at the same time.
1. Mai (uid:2488) v6.0b
proteinortho is now part of the bioconda repository
grab_proteins.pl makeover for brew integration
6. Mai (uid:2821) v6.0
finally proteinortho2xml.pl is working correctly.
clean up proteinortho_do_mcl.pl
renamed all files, such that every program starts with proteinortho !
11. Mai (uid:3023) v6.0.1
html improvement (now you can display alternative names from the fasta files)
refined error messages on duplicated inputs, <2 inputs
27. Juni (uid:3492)
proteinortho6.pl now writes databases (-step=1) into -tmp directory if system call failed.
fixed small issue that tmp directories are created inside eachother.
better stderr outputs e.g. if blast fails -> try -check ...
1. Juli (uid:3511)
fixed the -ram issue (used free memory, now total memory) in case there is a swap using up all free memory (also proteinortho_clustering now throws a warning not a error)
10. Juli (uid:3697)
fixed proteinortho_grab_proteins.pl: -tofiles option now escapes if -exact, replaced chomp with s/[\r\n]+$//
proteinortho_grab_proteins.pl speedup for -exact and a given proteinortho file
proteinortho6.pl replaced chomp with s/[\r\n]+$//
proteinortho_clustering.cpp fix bug that only uses lapack if -pld is set, regardless of the value.
