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http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences.
Proper citation: Genome Reference Consortium (RRID:SCR_006553) Copy
Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.
Proper citation: Dictyostelium discoideum genome database (RRID:SCR_006643) Copy
DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China.
Proper citation: Descriptions of Plant Viruses (RRID:SCR_006656) Copy
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
http://www.sanger.ac.uk/science/tools/seqtools
Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.
Proper citation: Belvu (RRID:SCR_015989) Copy
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Proper citation: Aevol (RRID:SCR_015966) Copy
https://bioinf.eva.mpg.de/anfo/
Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.
Proper citation: Anfo (RRID:SCR_015972) Copy
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
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
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
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
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
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
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
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
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
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
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
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
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
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