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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
https://cran.r-project.org/web/packages/lme4/index.html
Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."
Proper citation: lme4 (RRID:SCR_015654) Copy
http://www.sanger.ac.uk/science/tools/ssaha2-0
A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.
Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy
http://decgpu.sourceforge.net/homepage.htm
Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.
Proper citation: DecGPU (RRID:SCR_000585) Copy
http://www.bioinf.uni-leipzig.de/Software/RNAplex/
Software tool to rapidly search for short interactions between two long RNAs.
Proper citation: RNAplex (RRID:SCR_002763) Copy
http://bamview.sourceforge.net/
A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.
Proper citation: BamView (RRID:SCR_004207) Copy
http://noble.gs.washington.edu/proj/genomedata/
A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.
Proper citation: Genomedata (RRID:SCR_004544) Copy
http://alchemy.sourceforge.net/
ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.
Proper citation: ALCHEMY (RRID:SCR_005761) Copy
http://www.atgc-montpellier.fr/mpscan/
Web tool for index free mapping of multiple short reads on a genome.
Proper citation: MPscan (RRID:SCR_000587) Copy
https://github.com/almorlio/CiLiQuant
Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.
Proper citation: CiLiQuant (RRID:SCR_019319) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
http://sourceforge.net/projects/skewer/
Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
Proper citation: skewer (RRID:SCR_001151) Copy
http://www.ccmb.med.umich.edu/ccdu/SNPAAMapper
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take
Proper citation: SNPAAMapper (RRID:SCR_002012) Copy
A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile.
Proper citation: Identifiers.org (RRID:SCR_003735) Copy
https://bioconductor.org/packages/ggtree/
Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.
Proper citation: ggtree (RRID:SCR_018560) Copy
http://www.e-crisp.org/E-CRISP/
Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours.
Proper citation: E-CRISP (RRID:SCR_019088) Copy
Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.
Proper citation: NMRProcFlow (RRID:SCR_016592) Copy
http://bioinformatics.istge.it/cldb/indexes.html
Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.
Proper citation: Hyper Cell Line Database (RRID:SCR_007730) Copy
https://crispy.secondarymetabolites.org
Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction.
Proper citation: CRISPy-web (RRID:SCR_017970) Copy
http://sysbio.rnet.missouri.edu/multicom_toolbox/NNCon%201.0.html
Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.
Proper citation: NNcon (RRID:SCR_014292) Copy
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