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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
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
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
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://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
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://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
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://github.com/hyattpd/Prodigal
Software tool for protein coding gene prediction for prokaryotic genomes.
Proper citation: Prodigal (RRID:SCR_011936) Copy
http://www.ebi.ac.uk/~zerbino/oases/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Proper citation: Oases (RRID:SCR_011896) Copy
https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/rnnotator
Software designed to assemble Illumina single or paired-end reads.
Proper citation: Rnnotator (RRID:SCR_011897) Copy
http://opal.biology.gatech.edu/GeneMark/
A family of gene prediction programs developed at Georgia Institute of Technology.
Proper citation: GeneMark (RRID:SCR_011930) Copy
http://genome.cshlp.org/content/20/10/1432.full
A de novo transcriptome assembly from next-generation sequencing data.
Proper citation: STM (RRID:SCR_011898) Copy
http://tophat.cbcb.umd.edu/fusion_index.html
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy
http://www.cbcb.umd.edu/software/glimmer-mg/
A software system for finding genes in environmental shotgun DNA sequences.
Proper citation: Glimmer-MG (RRID:SCR_011932) Copy
http://whale.bio.titech.ac.jp/metagene/
A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaGeneAnnotator (RRID:SCR_011934) Copy
http://www.cse.sc.edu/~elallali/research/MGC.html
A software application for finding complete and incomplete genes in metagenomic reads.
Proper citation: MGC (RRID:SCR_011935) Copy
http://ab.inf.uni-tuebingen.de/software/metasim/
A Sequencing Simulator for Genomics and Metagenomics.
Proper citation: MetaSim (RRID:SCR_011940) Copy
http://ab.inf.uni-tuebingen.de/software/megan/
Software for analyzing metagenomes.
Proper citation: MEGAN (RRID:SCR_011942) Copy
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