mpiBLAST: Open-Source Parallel BLAST

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Legacy versions:

The following versions of mpiBLAST are no longer being actively developed. They are listed here for completeness and understanding of the evolution of the project. We highly recommend not running any of these older versions.


mpiBLAST-1.5.0-PIO mpiBLAST-1.5.0-pio.tar.gz

  • Included a more advanced parallel I/O technique
  • Added explicit database caching
  • Codebase deprecated in favor of version 1.6.0


mpiBLAST-1.5.0 beta1 mpiBLAST-1.5.0beta1.tgz

  • Added option to approximate e-values to significantly reduce time to calculate effective lengths
  • Never officially released as production quality
  • Codebase deprecated in favor of version 1.5.0-PIO


mpiBLAST-1.4.0-PIO mpiBLAST-1.4.0-pio.tgz

  • Includes parallel I/O features to version 1.4.0
  • Able to run on IBM BG/L with appropriate patch
  • Codebase deprecated in favor of version 1.5.0-PIO


mpiBLAST-1.4.0 mpiBLAST-1.4.0.tgz

  • Fixes performance issue of version 1.3.0
  • Results output in same order as NCBI blastall
  • Fragments copied more efficiently
  • Only portions of the result target sent to allow for large sequences to be output
  • Codebase deprecated in favor of version 1.5.0-PIO


mpiBLAST-1.3.0 mpiBLAST-1.3.0.tgz

  • Uses October 2004 NCBI Toolkit
  • Supports 250 database fragments
  • E-values calculated with effective length resulting in near-identical scores
  • Pipelines query to handle large query sets
  • Pipelines database access for shared storage to reduce thrashing
  • Can copy databases using MPI (when no shared storage) or not all (if fast parallel file-system)
  • mpiformatdb uses reordering to create near identically sized fragments
  • Users observed significant performance loss using this version
  • Codebase deprecated in favor of version 1.4.0


mpiBLAST-1.2.1 mpiBLAST-1.2.1.tgz

  • Uses November 2003 NCBI Toolkit
  • Codebase deprecated in favor of version 1.3.0


mpiBLAST-1.2.0 mpiBLAST-1.2.0.tgz

  • 64-bit capable
  • When writing results, mpiblast uses the distributed database fragments instead of the ones in shared storage.
  • blastx, tblastn, tblastx supported
  • mpiblast web interface included
  • Bug fix: resolved crashes when using -m 7,8,9 formats
  • Uses April 2003 NCBI Toolkit
  • Codebase deprecated in favor of version 1.2.1


mpiBLAST-1.1.1 mpiBLAST-1.1.1.tgz

  • Numerous bug fixes and memory leaks addressed
  • Better formatting of database into equal portions
  • Codebase deprecated in favor of version 1.2.0


mpiBLAST-1.1.0 mpiBLAST-1.1.0.tgz

  • Ported to Windows
  • mpiformatdb rewritten to use NCBI library
  • Codebase deprecated in favor of version 1.1.1


mpiBLAST-1.0.1 mpiBLAST-1.0.1.tgz

  • Bug fix: resolved crash when database formatted without indices
  • Added support 1000 fragments
  • Codebase deprecated in favor of version 1.1.0


mpiBLAST-1.0.0 mpiBLAST-1.0.0.tgz

  • Databases are distributed dynamically as needed.
  • NCBI library is used to process output.
  • E-values are adjusted based on database size for blastn only.
  • Codebase deprecated in favor of version 1.0.1


mpiBLAST-0.9 mpiBLAST-0.9.tgz

  • The initial release of mpiBLAST shows that database fragmentation was viable.
  • The fragments are distributed during the formatting process.
  • Output is processed by parser.
  • E-values are not adjusted.
  • Codebase deprecated in favor of version 1.0.0
 
 
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