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http://evolution.genetics.washington.edu/phylip.html

A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems.

Proper citation: PHYLIP (RRID:SCR_006244) Copy   

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http://stormo.wustl.edu/ScerTF

Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region.

Proper citation: ScerTF (RRID:SCR_006121) Copy   

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http://www-bionet.sscc.ru/sitex/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms.

Proper citation: SitEx (RRID:SCR_006122) Copy   

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https://compbio.dfci.harvard.edu/predictivenetworks//

A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.

Proper citation: Predictive Networks (RRID:SCR_006110) Copy   

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http://brainvis.wustl.edu/wiki/index.php/Caret:About

Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.

Proper citation: Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) Copy   

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http://202.38.126.151:8080/SDisease/

Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser.

Proper citation: SpliceDisease (RRID:SCR_006130) Copy   

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http://www.chemspider.com/

Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications.

Proper citation: ChemSpider (RRID:SCR_006360) Copy   

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http://cran.r-project.org/web/packages/QCGWAS/

Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies.

Proper citation: QCGWAS (RRID:SCR_006408) Copy   

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http://iubio.bio.indiana.edu/webapps/SeWeR/

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C.

Proper citation: SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) Copy   

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http://code.google.com/p/perm/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Proper citation: PerM (RRID:SCR_004223) Copy   

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http://bioinfo.au.tsinghua.edu.cn/software/TAGS/

Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TAGS (RRID:SCR_004294) Copy   

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http://kwanlab.bio.cuhk.edu.hk/BSRD/

A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets.

Proper citation: BSRD (RRID:SCR_004249) Copy   

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http://code.google.com/p/rna-star/

Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

Proper citation: STAR (RRID:SCR_004463) Copy   

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http://neuro.debian.net/

Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.

Proper citation: neurodebian (RRID:SCR_004401) Copy   

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

Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.

Proper citation: NCBI BioSystems Database (RRID:SCR_004690) Copy   

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http://www.ebi.ac.uk/QuickGO/

A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services.

Proper citation: QuickGO (RRID:SCR_004608) Copy   

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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   

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http://www.smpdb.ca/

An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable.

Proper citation: Small Molecule Pathway Database (RRID:SCR_004844) Copy   

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http://www.picsl.upenn.edu/ANTS/

Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.

Proper citation: ANTS - Advanced Normalization ToolS (RRID:SCR_004757) Copy   

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

Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database.

Proper citation: NCBI Probe (RRID:SCR_004816) Copy   

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