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http://www.phenosystems.com/www/index.php/products/gensearchngs

An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.

Proper citation: GensearchNGS (RRID:SCR_010802) Copy   

•   Source: SciCrunch Registry

http://www.insilicase.co.uk/agile/AgileVariantMapper.aspx

Software that visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals.

Proper citation: AgileVariantMapper (RRID:SCR_010770) Copy   

•   Source: SciCrunch Registry

https://github.com/BUStools/bustools/

Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.

Proper citation: Bustools (RRID:SCR_018210) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

https://github.com/blackrim/phyutility

Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.

Proper citation: Phyutility (RRID:SCR_018545) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/canu

Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Proper citation: Canu (RRID:SCR_015880) Copy   

•   Source: SciCrunch Registry

https://github.com/cmayer/BaitFisher-package

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

Proper citation: Baitfisher (RRID:SCR_015985) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Bio-Tradis

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

Proper citation: Bio-tradis (RRID:SCR_015993) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.barrnap.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Barrnap (RRID:SCR_015995) Copy   

•   Source: SciCrunch Registry

http://standage.github.io/AEGeAn

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

Proper citation: Aegean (RRID:SCR_015965) Copy   

•   Source: SciCrunch Registry

https://github.com/EvolBioInf/andi

Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.

Proper citation: andi (RRID:SCR_015971) Copy   

•   Source: SciCrunch Registry

http://disulfind.dsi.unifi.it/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

Proper citation: DISULFIND (RRID:SCR_016072) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/vboza/deepnano

Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.

Proper citation: DeepNano (RRID:SCR_016070) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/FALCON

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

Proper citation: Falcon (RRID:SCR_016089) Copy   

•   Source: SciCrunch Registry

https://github.com/osallou/cassiopee-c

Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.

Proper citation: Cassiopee (RRID:SCR_016056) Copy   

•   Source: SciCrunch Registry

http://cdbfasta.sourceforge.net/

Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.

Proper citation: Cdbfasta (RRID:SCR_016057) Copy   

•   Source: SciCrunch Registry

http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bio++ (RRID:SCR_016055) Copy   

•   Source: SciCrunch Registry

http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

Proper citation: Clonalframe (RRID:SCR_016060) Copy   

•   Source: SciCrunch Registry