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http://bpg.utoledo.edu/~afedorov/lab/eid.html

Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.

Proper citation: EID: Exon-Intron Database (RRID:SCR_002469) Copy   

•   Source: SciCrunch Registry

http://www.microbesonline.org/fasttree/

Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.

Proper citation: FastTree (RRID:SCR_015501) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/phytools/index.html

Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.

Proper citation: phytools (RRID:SCR_015502) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=cluster

Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.

Proper citation: Cluster (RRID:SCR_013505) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.org/ghemical/ghemical/index.html

Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms.

Proper citation: Ghemical (RRID:SCR_014899) Copy   

•   Source: SciCrunch Registry

http://huttenhower.sph.harvard.edu/galaxy

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LEfSe (RRID:SCR_014609) Copy   

•   Source: SciCrunch Registry

http://www.rdkit.org/

An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.

Proper citation: RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/fastahack

Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.

Proper citation: Fastahack (RRID:SCR_016090) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Fastaq

Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.

Proper citation: Fastaq (RRID:SCR_016091) Copy   

•   Source: SciCrunch Registry

http://fastqtl.sourceforge.net/

Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq.

Proper citation: Fastqtl (RRID:SCR_016093) Copy   

•   Source: SciCrunch Registry

http://harvest.readthedocs.org/en/latest/content/harvest-tools.html

Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations.

Proper citation: Harvest-tools (RRID:SCR_016132) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/alien-hunter

Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.

Proper citation: Alien-hunter (RRID:SCR_015967) Copy   

•   Source: SciCrunch Registry

https://pynwb.readthedocs.io/en/latest/

Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.

Proper citation: PyNWB (RRID:SCR_017452) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html

Software application (entry from Genetic Analysis Software)

Proper citation: FASTLINK (RRID:SCR_009177) Copy   

•   Source: SciCrunch Registry

http://www.rqtl.org

Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software)

Proper citation: R/QTL (RRID:SCR_009085) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Minimac

Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)

Proper citation: MINIMAC (RRID:SCR_009292) Copy   

•   Source: SciCrunch Registry

http://evolution.genetics.washington.edu/lamarc/lamarc_prog.html

Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software)

Proper citation: LAMARC (RRID:SCR_009252) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/peer/

Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python.

Proper citation: PEER (RRID:SCR_009326) Copy   

•   Source: SciCrunch Registry

http://hadoop.apache.org/

Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.

Proper citation: Apache Hadoop (RRID:SCR_011879) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry