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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://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

https://dazzlerblog.wordpress.com

Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.

Proper citation: Daligner (RRID:SCR_016066) Copy   

•   Source: SciCrunch Registry

http://hyphy.org/

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

Proper citation: HyPhy (RRID:SCR_016162) Copy   

•   Source: SciCrunch Registry

http://abacus.gene.ucl.ac.uk/software/indelible/

Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.

Proper citation: Indelible (RRID:SCR_016163) Copy   

•   Source: SciCrunch Registry

http://fastml.tau.ac.il/

Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.

Proper citation: Fastml (RRID:SCR_016092) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/gubbins/

Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gubbins (RRID:SCR_016131) Copy   

•   Source: SciCrunch Registry

http://www.zucic.org/garlic/

Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.

Proper citation: Garlic (RRID:SCR_016118) Copy   

•   Source: SciCrunch Registry

http://www.fishbrowser.org/software/LR_Gapcloser/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies.

Proper citation: LR Gapcloser (RRID:SCR_016194) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.

Proper citation: Dotter (RRID:SCR_016080) Copy   

•   Source: SciCrunch Registry

http://genome.imim.es/software/gfftools/GFF2APLOT.html

Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis.

Proper citation: Gff2aplot (RRID:SCR_016128) Copy   

•   Source: SciCrunch Registry

http://gentle.magnusmanske.de

Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.

Proper citation: Gentle (RRID:SCR_016127) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Exonerate (RRID:SCR_016088) Copy   

•   Source: SciCrunch Registry

https://huttenhower.sph.harvard.edu/humann2

Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.

Proper citation: HUMAnN2 (RRID:SCR_016280) Copy   

•   Source: SciCrunch Registry

https://github.com/Teichlab/tracer

Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles.

Proper citation: TraCeR (RRID:SCR_016338) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.brown.edu/projects/gasv/

Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments.

Proper citation: GASVPro (RRID:SCR_005259) Copy   

•   Source: SciCrunch Registry

http://www.bioextract.org/GuestLogin

An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

Proper citation: BioExtract (RRID:SCR_005397) Copy   

•   Source: SciCrunch Registry

http://statgenpro.psychiatry.hku.hk/limx/kggseq/

A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.

Proper citation: KGGSeq (RRID:SCR_005311) Copy   

•   Source: SciCrunch Registry

http://www.yandell-lab.org/software/mwas.html

The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally.

Proper citation: MAKER Web Annotation Service (RRID:SCR_005318) Copy   

•   Source: SciCrunch Registry

http://users-birc.au.dk/biopv/php/fabox/

Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER.

Proper citation: FaBox (RRID:SCR_005350) Copy   

•   Source: SciCrunch Registry