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http://biolemmatizer.sourceforge.net/
A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.
Proper citation: BioLemmatizer (RRID:SCR_000117) Copy
http://www.bioconductor.org/packages/release/bioc/html/ReQON.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.
Proper citation: ReQON (RRID:SCR_000075) Copy
http://www.iro.umontreal.ca/~csuros/quadgt/
Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.
Proper citation: QuadGT (RRID:SCR_000073) Copy
http://soap.genomics.org.cn/soapfuse.html
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .
Proper citation: SOAPfuse (RRID:SCR_000078) Copy
http://www.gobics.de/fabian/treephyler.php
A software tool for fast taxonomic profiling of metagenomes.
Proper citation: Treephyler (RRID:SCR_000109) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html
Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
Proper citation: GenomicRanges (RRID:SCR_000025) Copy
Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).
Proper citation: JChemPaint (RRID:SCR_000095) Copy
An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design.
Proper citation: DOCK (RRID:SCR_000128) Copy
http://sourceforge.net/projects/exomesuite/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.
Proper citation: exomeSuite (RRID:SCR_000129) Copy
http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html
Software package for various databases of microRNA Targets.
Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy
https://code.google.com/p/nfuse/
Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).
Proper citation: nFuse (RRID:SCR_000066) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/
Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy
A multiple-sample, technology-aware SNP and indel caller.
Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075146
An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.
Proper citation: NuChart (RRID:SCR_004703) Copy
http://matsen.fhcrc.org/pplacer/
Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
Proper citation: Pplacer (RRID:SCR_004737) Copy
Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.
Proper citation: TETRA (RRID:SCR_004573) Copy
https://sites.google.com/a/lbl.gov/biopig/
Software providing a framework for genomic data analysis using Apache Pig and Hadoop.
Proper citation: BioPig (RRID:SCR_004636) Copy
https://github.com/lmrodriguezr/nonpareil
Estimate average coverage and create Nonpareil curves for metagenomic datasets.
Proper citation: Nonpareil (RRID:SCR_004629) Copy
http://omics.informatics.indiana.edu/AbundanceBin/
An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.
Proper citation: AbundanceBin (RRID:SCR_004648) Copy
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