Tools   Select Another Resource Report Type

http://ccb.jhu.edu/software/glimmer/index.shtml

A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Proper citation: Glimmer (RRID:SCR_011931) Copy   

•   Source: SciCrunch Registry

http://www.jcvi.org/metarep/

A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.

Proper citation: METAREP (RRID:SCR_011926) Copy   

•   Source: SciCrunch Registry

http://cpfp.sourceforge.net/

Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.

Proper citation: CPFP (RRID:SCR_012043) Copy   

•   Source: SciCrunch Registry

https://github.com/MikkelSchubert/adapterremoval

Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.

Proper citation: AdapterRemoval (RRID:SCR_011834) Copy   

•   Source: SciCrunch Registry

http://opm.phar.umich.edu/

Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.

Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy   

•   Source: SciCrunch Registry

http://srna-workbench.cmp.uea.ac.uk/tools/visualisation-tools/vissr/

Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat.

Proper citation: VisSR (RRID:SCR_012024) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/ariba

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

Proper citation: Ariba (RRID:SCR_015976) Copy   

•   Source: SciCrunch Registry

http://kmer.sourceforge.net

Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.

Proper citation: Atac (RRID:SCR_015980) Copy   

•   Source: SciCrunch Registry

http://www.ball-project.org/ballview

Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

Proper citation: BALLView (RRID:SCR_015986) Copy   

•   Source: SciCrunch Registry

https://github.com/kdmurray91/axe

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

Proper citation: Axe (RRID:SCR_015984) Copy   

•   Source: SciCrunch Registry

https://github.com/pezmaster31/bamtools/wiki

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

Proper citation: Bamtools (RRID:SCR_015987) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/SimonHTausch/HiLive

Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.

Proper citation: HiLive (RRID:SCR_016134) Copy   

•   Source: SciCrunch Registry

http://mbio-serv2.mbioekol.lu.se/ARAGORN/

Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Aragorn (RRID:SCR_015974) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/arden/

Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.

Proper citation: Arden (RRID:SCR_015975) Copy   

•   Source: SciCrunch Registry

http://fsa.sourceforge.net/

Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned.

Proper citation: FSA (RRID:SCR_016114) Copy   

•   Source: SciCrunch Registry

https://github.com/Ashod/garli

Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.

Proper citation: GARLI (RRID:SCR_016117) Copy   

•   Source: SciCrunch Registry

https://github.com/nvalimak/fsm-lite

Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data.

Proper citation: Fsm-lite (RRID:SCR_016115) Copy   

•   Source: SciCrunch Registry

https://github.com/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php

Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame.

Proper citation: gdpc (RRID:SCR_016119) Copy   

•   Source: SciCrunch Registry

http://zhanglab.ccmb.med.umich.edu/EDTSurf/

Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.

Proper citation: Edtsurf (RRID:SCR_016083) Copy   

•   Source: SciCrunch Registry