This release is a pre-release and may not be stable for production use.
SonicParanoid
A fast, accurate and easy to use orthology inference tool.
Description
SonicParanoid is a stand-alone software for the identification of orthologous relationships among multiple species. SonicParanoid is an open source software released under the GNU GENERAL PUBLIC LICENSE, Version 3.0 (GPLv3), implemented in Python3, Cython, and C++. It works on Linux and Mac OSX. The software is designed to run using multiple processors and proved to be up to 1245X faster then InParanoid, 166X faster than Proteinortho, and 172X faster than OrthoFinder 2.0 with an accuracy comparable to that of well-established orthology inference tools. Thanks to its speed, accuracy, and usability SonicParanoid substantially relieves the difficulties of orthology inference for biologists who need to construct and maintain their own genomic datasets.
SonicParanoid was tested on the 2011 version of a benchmark proteome dataset provided by the Quest for Orthologs (QfO) consortium (https://questfororthologs.org), and its accuracy was assessed, and compared to that of other 13 methods, using a publicly available orthology benchmarking service (http://orthology.benchmarkservice.org).
SonicParanoid is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid.
Citation
> Salvatore Cosentino and Wataru Iwasaki (2018) SonicParanoid: fast, accurate and easy orthology inference. Bioinformatics
> Volume 35, Issue 1, 1 January 2019, Pages 149–151,
Changelog
- 1.3.0 (October XX, 2019)
Enhancement: SonicParanoid is mcuh faster! Check the web-page…
Enhancement: run directory names embed information on the run settings
Others: Big thanks to Shun Yamanouchi for providing the bacterial datasets used for testing
Fix: force overwriting of MMseqs2 binaries if the version is different from the supported one
Maintenance: upgraded to MMseqs2 version 10-6d92c
- 1.2.6 (August 26, 2019)
Fix: "to many files open" error which sometimes happened when using more than 20 threads
- 1.2.5 (August 7, 2019)
Fix: Logical threads are considered instead of physical cores in the adjustment of the threads number
Requirements: a minimum of 1.75 gigabytes per thread is required (the number of threads is automatically adjusted)
Enhancement: added parameter --force-all-threads to bypass the check for minimum per-thread memory
- 1.2.4 (July 14, 2019)
Enhancement: Added control to avoid selecting a number threads higher than the available physical CPU cores (big thanks to Shun Yamanouchi)
Fix: Removed some scipy warnings, now shown only in debug mode (thanks to Alexie Papanicolaou)
Requirements: psutils>=5.6.0 is now required
Requirements: mypy>=0.701 is now required
Requirements: at least Python 3.6 is now required
- 1.2.3 (June 7, 2019)
Enhancement: some error messages are more informative (big thanks to Jeff Stein)
- 1.2.2 (May 13, 2019)
Fix: solved a bug that caused MCL to be not properly compiled on some Linux distributions
Info: source code migrated to GitLab
- 1.2.1 (May 10, 2019)
Fix: solved bug related to random missing alignments
Info: this issue was first described in here
- 1.2.0 (April 26, 2019)
Change: Markov Clustering (MCL) is now used by default for the creation of ortholog groups
Enhancement: the MCL inflation can be controlled through the parameter --inflation
Enhancement: Output file with single-copy ortholog groups
Feature: single-linkage clustering for ortholog groups creation through the --single-linkage parameter
Enhancement: added secondary program to filter ortholog groups
Info: type sonicparanoid-extract --help to see the list of options
Enhancement: Filter ortholog groups by species ID
Enhancement: Filter ortholog groups by species composition (e.g., only groups with given number of species)
Enhancement: Extract FASTA sequences of orthologs in selected groups
Fix: The correct version of SonicParanoid is now shown in the help
Others: General bug fixes and under-the-hood improvements
- 1.1.2 (March, 2019)
Enhancement: Filter ortholog groups by species ID
Enhancement: Filter ortholog groups by species composition (e.g., only groups with given number of species)
Enhancement: Extract FASTA files corresponding orthologs in selected groups
Fix: The correct version of SonicParanoid is now shown in the help
- 1.1.1 (January 24, 2019)
Enhancement: No restriction on file names
Enhancement: No restriction on symbols used in FASTA headers
Enhancement: Added file with genes that could not be inserted in any group (not orthologs)
Enhancement: Added some statistics on the predicted ortholog groups
Enhancement: Update runs are automatically detected
Enhancement: Improved inference of in-paralogs
Change: The directory structure has been redesigned to better support run updated
- 1.0.14 (October 19, 2018)
Enhancement: a warning is shown if non-protein sequences are given in input
Enhancement: upgraded to MMseqs2 6-f5a1c
Enhancement: SonicParanoid is now available through Bioconda (https://bioconda.github.io/recipes/sonicparanoid/README.html)
- 1.0.13 (September 18, 2018)
Fix: allow FASTA headers containing the ‘@’ symbol
- 1.0.12 (September 7, 2018)
Improved accuracy
Added new sensitivity mode (most-sensitive)
Fix: internal input directory is wiped at every new run
Fix: available disk space calculation
- 1.0.11 (August 7, 2018)
Added new program (sonicparanoid-extract) to process output multi-species clusters
Added the possibility to analyse only 2 proteomes
Added support for Python3.7
Python3 versions: 3.5, 3.6, 3.7
Upgraded MMseqs2 (commit: a856ce, August 6, 2018)
- 1.0.9 (May 10, 2018)
First public release
Python3 versions: 3.4, 3.5, 3.6
1 maintainer
Release files for sonicparanoid 1.3.0b6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sonicparanoid-1.3.0b6.tar.gz | 37.3 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sonicparanoid-1.3.0b6-cp37-cp37m-macosx_10_15_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | macOS 10.15+ x86-64 | Details |
Total release size: 75.2 MB
Release files / sonicparanoid-1.3.0b6.tar.gz
| Download URL | sonicparanoid-1.3.0b6.tar.gz |
|---|---|
| Size | 37.3 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
b17f05530fd54482b2d58b365d3e10719775caeb8d7ec913d2ce628c3c76bee5
|
|
BLAKE2b-256 checksum How to use checksums |
bfe8b6f39c2173d655c8ad298752679d13fd56bb794bbe76d534b39ab2b5aee1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/2.0.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.6.0 requests-toolbelt/0.9.1 tqdm/4.38.0 CPython/3.7.5
|
Release files / sonicparanoid-1.3.0b6-cp37-cp37m-macosx_10_15_x86_64.whl
| Download URL | sonicparanoid-1.3.0b6-cp37-cp37m-macosx_10_15_x86_64.whl |
|---|---|
| Size | 37.9 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc macOS 10.15+ x86-64 |
|
SHA-256 checksum How to use checksums |
6dd32f923d11bad15d3f76705abdd84611e7c0aca399400313a30d719a921b6b
|
|
BLAKE2b-256 checksum How to use checksums |
97494c158f62a4d190d8f3c191f1ccd1239d7f5eb6e2da0dc3a83eb7933ed12c
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/2.0.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.6.0 requests-toolbelt/0.9.1 tqdm/4.38.0 CPython/3.7.5
|
