Curator Dashboard

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 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.

• Resource
• 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

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 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.

• Resource
• 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.

• Resource
• 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 tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in.

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• RRID-Legacy
• 9 years ago - by Anonymous

Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

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.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman