software package for designing hybrid enrichment probes

 The BaitFisher package consists of two programs: BaitFisher and BaitFilter.
 .
 BaitFisher was been designed to construct hybrid enrichment baits from
 multiple sequence alignments (MSAs) or annotated features in MSAs. The main
 goal of BaitFisher is to avoid redundancy in the construction of baits by
 designing fewer baits in conserved regions of the MSAs and designing more baits
 in variable regions. This makes use of the fact that hybrid enrichment baits
 can differ to some extends from the target region, which they should capture
 in the enrichment procedure.
 By specifying the allowed distance between baits and the sequences in the MSAs
 the user can control the allowed bait-to-target distance and the degree of
 reduction in the number of baits that are designed.
 See the BaitFisher paper for details.
 .
 BaitFilter was designed (i) to determine whether baits bind unspecifically to
 a reference genome, (ii) to filter baits that only have partial length matches
 to a reference genome, (iii) to determine the optimal bait region in a MSA and
 to convert baits to a format that can be uploaded at a bait constructing
 company. The optimal bait region can be the most conserved region in the MSA
 or the region with the highest number of sequences without gaps or ambiguous
 nucleotides.