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http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry
  

http://www.biopieces.org

A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014).

Proper citation: Biopieces (RRID:SCR_005783) Copy   

•   Source: SciCrunch Registry
  

http://segway.hoffmanlab.org/

The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy   

•   Source: SciCrunch Registry
  

http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html

VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, users can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures. * Search homologous protein families from particular virus families * Links to complete genome sequence: Arteriviridae, Coronaviridae, Herpesviridae, Poxviridae The Virus Database at University College London has been developed as a system to organize animal virus open reading frame sequences. All known and predicted protein sequences from complete and partial genomes of particular virus families are extracted from GenBank and filtered to remove 100% redundancy. On the basis of sequence similarity the sequences are then clustered into homologous protein families (HPFs). The families are enriched with annotations including function and functional classification, related protein structures, taxonomy, length of the proteins, boundaries of the conserved region/s, virus-specific gene name and links to EMBL entries and SWISSPROT., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VIDA (RRID:SCR_007111) Copy   

•   Source: SciCrunch Registry
  

http://cudasw.sourceforge.net/

CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher

Proper citation: CUDASW++ (RRID:SCR_008862) Copy   

•   Source: SciCrunch Registry
  

http://www-stat.stanford.edu/~tibs/SAM/

Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.

Proper citation: SAM (RRID:SCR_010951) Copy   

•   Source: SciCrunch Registry
  

http://bioen-compbio.bioen.illinois.edu/FusionHunter/

Software for identifying fusion transcripts using paired-end RNA-seq.

Proper citation: FusionHunter (RRID:SCR_011895) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.com/kyrgyzov/lsa_slurm

Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics.

Proper citation: lsa_slurm (RRID:SCR_018134) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Pithikos/C-Thread-Pool

Software for minimal but powerful thread pool in ANSI C.

Proper citation: C Thread Pool (RRID:SCR_023999) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nexml/nexml.java

Software repository contains java code for NeXML processing.

Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy   

•   Source: SciCrunch Registry
  

https://github.com/smirarab/sepp/

Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.

Proper citation: sepp (RRID:SCR_024327) Copy   

•   Source: SciCrunch Registry
  

https://www.teuniz.net/edflib/

Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.

Proper citation: EDFlib (RRID:SCR_024010) Copy   

•   Source: SciCrunch Registry
  

http://www.dclunie.com/dicom3tools.html

Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.

Proper citation: Dicom3tools (RRID:SCR_024008) Copy   

•   Source: SciCrunch Registry
  

https://github.com/stamatak/AxPcoords.dist

Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.

Proper citation: AxPcoords (RRID:SCR_023971) Copy   

•   Source: SciCrunch Registry
  

http://sco.h-its.org/exelixis/web/software/AxParafit/index.html

Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.

Proper citation: AxParafit (RRID:SCR_023968) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nextstrain/auspice

Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.

Proper citation: Auspice (RRID:SCR_023966) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sanger-pathogens/assembly-stats

Software to get assembly statistics from FASTA and FASTQ files.

Proper citation: assembly-stats (RRID:SCR_023963) Copy   

•   Source: SciCrunch Registry
  

https://github.com/thegenemyers/DEXTRACTOR

Software as Bax file decoder and data compressor.

Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/thornton-srv/databases/WSsas/

SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions.

Proper citation: WSsas - Web Service for the SAS tool (RRID:SCR_007051) Copy   

•   Source: SciCrunch Registry
  

http://ani.embl.de/4DXpress

This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data.

Proper citation: Expression Database in 4D (RRID:SCR_007066) Copy   

•   Source: SciCrunch Registry