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Bio-MUST-Drivers-0.242720
River stage one • 4 direct dependents • 4 total dependents

Changes for version 0.242720 - 2024-09-28

  • Additions
    • Blast: expanded list of supported remote databases (e.g., core_nt)
    • Mafft: added support for options --addlong and --addfragments
    • binaries: new script annotate-ali.pl
  • Changes
    • Blast: upgraded driver to better handle version 5 of BLAST databases
  • Fixes
    • Blast: updated tests to BLAST 2.16.0
    • Mafft: fixed command-line bug with align_all method

Modules

Bio::MUST::Drivers
Bio::MUST classes for driving external programs
Bio::MUST::Drivers::Blast
Bio::MUST driver for running the NCBI-BLAST+ suite of programs
Bio::MUST::Drivers::Blast::Database
Internal class for BLAST driver
Bio::MUST::Drivers::Blast::Database::Temporary
Internal class for BLAST driver
Bio::MUST::Drivers::Cap3
Bio::MUST driver for running the CAP3 assembly program
Bio::MUST::Drivers::CdHit
Bio::MUST driver for running the CD-HIT program
Bio::MUST::Drivers::ClustalO
Bio::MUST driver for running the Clustal Omega program
Bio::MUST::Drivers::Exonerate
Bio::MUST driver for running the Exonerate alignment program
Bio::MUST::Drivers::Exonerate::Aligned
Bio::MUST driver for running the Exonerate alignment program
Bio::MUST::Drivers::Exonerate::Sugar
Internal class for exonerate driver
Bio::MUST::Drivers::Hmmer
Bio::MUST driver for running HMMER3
Bio::MUST::Drivers::Hmmer::Model
Internal class for HMMER3 driver
Bio::MUST::Drivers::Hmmer::Model::Database
Internal class for HMMER3 driver
Bio::MUST::Drivers::Hmmer::Model::Temporary
Internal class for HMMER3 driver
Bio::MUST::Drivers::Mafft
Bio::MUST driver for running the MAFFT program
Bio::MUST::Drivers::Roles::Blastable
BLAST database-related methods
Bio::MUST::Drivers::Roles::Hmmerable
HMMER model-related methods
Bio::MUST::Drivers::Utils
Utility functions for drivers
Bio::MUST::Provision::Blast
Internal class for app provisioning system
Bio::MUST::Provision::Cap3
Internal class for app provisioning system
Bio::MUST::Provision::CdHit
Internal class for app provisioning system
Bio::MUST::Provision::ClustalO
Internal class for app provisioning system
Bio::MUST::Provision::Exonerate
Internal class for app provisioning system
Bio::MUST::Provision::Hmmer
Internal class for app provisioning system
Bio::MUST::Provision::Mafft
Internal class for app provisioning system

Other files