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https://github.com/genomeannotation/GAG
Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format.
Proper citation: Genome Annotation Generator (RRID:SCR_016053) Copy
https://savannah.gnu.org/projects/datamash/
Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.
Proper citation: Datamash (RRID:SCR_016067) Copy
https://github.com/jts/nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data.
Proper citation: Nanopolish (RRID:SCR_016157) Copy
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
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
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
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
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
Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.
Proper citation: GenomeTools (RRID:SCR_016120) Copy
Software for syntax highlighting for computational biology.
Proper citation: bioSyntax (RRID:SCR_016207) Copy
IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.
Proper citation: IDEPI - IDentify EPItopes (RRID:SCR_016171) Copy
https://odmltables.readthedocs.io
Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats.
Proper citation: odMLtables (RRID:SCR_016228) Copy
http://utgenome.org/index.html
An open-source software for developing personalized genome browsers that work in web browsers.
Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy
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
http://graphics.med.yale.edu/trim/
A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.
Proper citation: Btrim (RRID:SCR_011836) Copy
http://www.genome.umd.edu/quorum.html
Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
Proper citation: QuorUM (RRID:SCR_011840) Copy
http://code.google.com/p/cutadapt/
Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: cutadapt (RRID:SCR_011841) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
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
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
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