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BiGpairSEQ_Sim v4.4 Stable
efischer released this
2025-04-10 20:04:40 +00:00 | 3 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Refactored to construct bipartite graph directly rather than using an adjacency matrix, to (hopefully) reduce the memory required
Compatible with Graph/Data (.ser) files from:
BiGpairSEQ_Sim v4.2
BiGpairSEQ_Sim v4.3Downloads
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BiGpairSEQ_Sim v4.3 Stable
2025-04-09 21:18:57 +00:00 | 12 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Now uses pairing heap by default
- Added Zipf distribution to T cell frequency options
Compatible with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v4.2
Downloads
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BiGpairSEQ_Sim v4.2 Stable
2022-10-01 23:35:06 +00:00 | 56 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Calculation of p-values now off by default
- Updated and reorganized Readme
Compatible with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v4.2
Downloads
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BiGpairSEQ_Sim v4.1 Stable
2022-09-29 05:11:09 +00:00 | 87 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- When read errors are enabled, sequences can now be misread as other real sequences on the plate
Compatible with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v4.1
Downloads
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BiGpairSEQ_Sim v4.0 Stable
2022-09-28 08:04:15 +00:00 | 104 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Implemented simulation of sequence read depth and sequence read errors, to better match the behavior of actual sequencers.
- Added read depth data to graphml output.
- Refactored simulator code to be significantly simpler.
- Fixed bug in sequence occupancy counting; occupancies are now counted accurately.
Compatible with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v.4.0
Downloads
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BiGpairSEQ_Sim v3.0 Stable
2022-09-26 00:15:37 +00:00 | 171 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Custom Vertex class implemented to allow future implementation of different MWM algorithms. This change in underlying data structure also seems to speed up matching with the present MWM algorithm. (This change breaks compatibility with Graph/Data files from previous versions of BiGpairSEQ_sim.)
Compatible with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v.3.0
Downloads
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BiGpairSEQ_Sim v2.0 Stable
2022-02-27 23:02:15 +00:00 | 206 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Now supports command line arguments, to allow use in shell scripts. For full list of command line arguments, run the program with the
-helpflag.
Compatible with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v1.2
- BiGpairSEQ_Sim v1.3
- BiGpairSEQ_Sim v1.4
- BiGpairSEQ_Sim v1.5
- BiGpairSEQ_Sim v2.0
Downloads
- Now supports command line arguments, to allow use in shell scripts. For full list of command line arguments, run the program with the
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BiGpairSEQ_Sim v1.5 Stable
2022-02-26 17:08:18 +00:00 | 223 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- GraphML file output implemented for full data portability
- File output options added to Options menu
Compatibel with Graph/Data (.ser) files from:
- BiGpairSEQ_Sim v1.2
- BiGpairSEQ_Sim v1.3
- BiGpairSEQ_Sim v1.4
- BiGpairSEQ_Sim v1.5
Downloads
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BiGpairSEQ_Sim v1.4 Stable
2022-02-24 21:43:48 +00:00 | 239 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog:
- Default file caching behavior changed to OFF
- Default priority queue for MWM algorithm changed to Fibonacci heap
- Priority queue option menu implemented
Compatible with Graph data (.ser files) from:
- BiGpairSEQ_Sim v1.2
- BiGpairSEQ_Sim v1.3
- BiGpairSEQ_Sim v1.4
Downloads
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BiGpairSEQ_Sim v1.3 Stable
2022-02-24 18:53:32 +00:00 | 245 commits to master since this releaseExecutable .jar file for BiGpairSEQ simulator. See this release's readme.md file for description and usage instructions.
Changelog: file caching behavior now controllable from new Options menu.
Compatible with Graph data (.ser files) from:
- BiGpairSEQ_Sim v1.2
- BiGpairSEQ_Sim v1.3
Downloads