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Table 1 Software packages and libraries used within Ribovore v1.0

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

  1. *: the esl-cluster executable from Infernal v1.1.2, which is absent in v1.1.4, is also installed and used within Ribovore