Curator Dashboard

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.<br/>From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.<br/><br/>Software for streaming quantification for high-throughput DNA/RNA sequencing. <br/>Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package to perform Bayesian analysis of molecular sequences using a family of Markov Chain Monte Carlo (MCMC) algorithms. It can estimate phylogenies using a wide range of models.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

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• RRID-Legacy
• 9 years ago - by Anonymous

Dataset replicating the experiment done on BNCI-HORIZON 008-2014 dataset. BCI P300 Speller Kaggle Dataset for Healthy subjects

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• RRID-Legacy
• 9 years ago - by Anonymous

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.

• SciCrunch
• 9 years ago - submitted by Isabella Froman