From: Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
Software and website | Used within | Purpose in Ribovore |
---|---|---|
Sequip v0.08 github.com/nawrockie/sequip | All Ribovore programs | Option handling, output file handling and other utilities |
Infernal v1.1.4* github.com/EddyRivasLab/infernal | All Ribovore programs | Build and use profile HMMs and CMs to classify, validate and align rRNA sequences |
BLAST+ v2.11.0 ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/2.11.0 | Ribodbmaker | Build BLAST databases and validate rRNA sequences |
VecScreen_plus_taxonomy v0.17 github.com/aaschaffer/ vecscreen_plus_taxonomy | Ribodbmaker | Screen for vector contamination |
GNU time (not required) | All Ribovore programs if -p option is used | Determine running time |