├── LICENSE ├── Makefile ├── README.md ├── SA_BOND ├── readme.txt └── src │ └── sabond.cpp ├── bin ├── Assignment.pl ├── Clustering.pl ├── Config.pl ├── Filtering.pl ├── GetTargetRegions.pl ├── HUBDesign ├── Identification.pl └── Selection.pl ├── lib ├── Bio │ └── Align │ │ └── ParallelDNAStatistics.pm └── HUBDesign │ ├── BaitRegion.pm │ ├── Bipartition.pm │ ├── Grouping.pm │ ├── Logger.pm │ ├── ProgressBar.pm │ ├── Pseudorg.pm │ └── Util.pm ├── probes ├── Coronavirus │ ├── BaitInfo.tab │ ├── BaitSequence.fna.gz │ └── GuideTree.newick └── sepsis │ ├── BaitInfo.tsv │ └── Baits.fna ├── test ├── GenomeInfo.tab ├── Genomes │ ├── 1920748.gff.gz │ ├── 2697049.gff │ ├── 277944.gff │ ├── 694009.gff │ └── 864596.gff ├── Guide.tree └── output │ ├── ClustInfo.tsv │ ├── ClustSeq.fna │ ├── Guide.dend │ ├── ProbeInfo.tsv │ ├── Probes.fna │ └── intermediate_XXXX │ ├── Assignment.tsv │ ├── Candidates.tab │ ├── Filtered.tab │ ├── HUBDESIGN_CP_8f6i.olig │ ├── HUBDESIGN_PG_NlIE.fna │ └── 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