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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.phylotree.org/

A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature.

Proper citation: PhyloTree.org (RRID:SCR_012948) Copy   

•   Source: SciCrunch Registry
  

http://www.meta-analysis.com/index.php

A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity.

Proper citation: CMA (RRID:SCR_012779) 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
  

http://www.ncbi.nlm.nih.gov/medgen/

A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution.

Proper citation: MedGen (RRID:SCR_000111) Copy   

•   Source: SciCrunch Registry
  

http://wukong.tongji.edu.cn/pepid

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database to store the curated epigenetic data from studies of prostate cancer retrieved by literature mining. The Prostate Epigenetic Database (PEpiD) is meant as a resource for finding previous studies of prostate cancer in humans, mice and rats. Searches can be targeted through the categories of DNA methylation, histone modification, and microRNA.

Proper citation: PEpiD (RRID:SCR_000235) Copy   

•   Source: SciCrunch Registry
  

http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

Proper citation: ARNIE (RRID:SCR_000514) Copy   

•   Source: SciCrunch Registry
  

http://cbcsrv.watson.ibm.com/phylopythia.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments.

Proper citation: PhyloPythia (RRID:SCR_000540) Copy   

•   Source: SciCrunch Registry
  

http://apoptoproteomics.uio.no/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database of resources on cancer processes such as cell death. It is a subset of a larger database on cancer proteomics that focuses on anti-cancer drugs and cancer types in addition to cancer processes. It utilizes scientific articles from PubMed, UniProt and other resources along with information such as author information, sample types and useful hyperlinks.

Proper citation: Cell Death Proteomics Database (RRID:SCR_000200) Copy   

•   Source: SciCrunch Registry
  

http://bovinegenome.org/

Database and integrated tools to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data.

Proper citation: Bovine Genome Database (RRID:SCR_000148) Copy   

•   Source: SciCrunch Registry
  

http://pc1664.pharmazie.uni-marburg.de/affinity/

Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms:
# Summary information for PDB entry
# Affinity information window
# Tabular reports

Proper citation: AffinDB (RRID:SCR_001690) Copy   

•   Source: SciCrunch Registry
  

http://www.bioguo.org/AnimalTFDB/

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: AnimalTFDB (RRID:SCR_001624) Copy   

•   Source: SciCrunch Registry
  

https://www.hgmd.cf.ac.uk/ac/introduction.php?lang=english

Curated database of known (published) gene lesions responsible for human inherited disease.

Proper citation: Human Gene Mutation Database (RRID:SCR_001621) Copy   

•   Source: SciCrunch Registry