BaitsTools specifications


Unique identifier OMICS_22253
Name BaitsTools
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A sequence file or population summary statistics files, or genome annotations or features and ipyrad loci files.
Output data A set of filtered baits and an optional files describing (i) the location of filtered baits with regard to the input reference sequences and (ii) a summary that tabulates the filtration parameters and inclusion/exclusion from the final filtered bait set for each candidate bait.
Output format FASTA/BED
Operating system Unix/Linux, Mac OS
Programming languages Ruby, Shell (Bash)
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes




No version available



  • person_outline Michael Campana

Additional information

A GUI is available on MacOS only.

Publication for BaitsTools

BaitsTools citation


Marker Development for Phylogenomics: The Case of Orobanchaceae, a Plant Family with Contrasting Nutritional Modes

Front Plant Sci
PMCID: 5704539
PMID: 29218053
DOI: 10.3389/fpls.2017.01973

[…] . and developed MarkerMiner 1.0 and BaitFisher, respectively. Both tools provide an automated, user-friendly and web-supported workflow for discovery of LCN loci from transcriptome data. developed BaitsTools, which automates bait design from various sources (e.g., alignments, unaligned sequences, and RADseq loci) and quality checking of thus obtained baits. Disadvantages of these approaches inc […]

BaitsTools institution(s)
Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
BaitsTools funding source(s)
Supported by The National Science Foundation (award DEB- 1547168), the Morris Animal Foundation (award D14ZO-308), and the National Geographic Society (award 8846-10).

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