A software package for designing hybrid enrichment baits. BaitFisher consists of two programs: BaitFisher and BaitFilter. The main goal of BaitFisher is to avoid redundancy in the construction of baits by designing fewer baits in conserved regions of the multiple sequence alignments (MSA) and designing more baits in variable regions. 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.
Allows users to handle high-throughput amplicon-sequencing data. SEED2 can serve for batch processing of fasta and fastq files specific for amplicon sequencing studies. It aims to simplify clustering, quality filtering/trimming, taxonomic identification, creation and description of molecular taxa and their phylogenetic placements. It also can be used for assessment of basic microbial community statistics.
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