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Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes.

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

Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

University in Durham, England.

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

University in Bratislava, Slovakia.

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

Software for handling multimedia files. FFmpeg can record, convert and stream audio and video.

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• RRID-Legacy
• 9 years ago - submitted by Samuel Nastase

Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html

• RRID-Legacy
• 9 years ago - submitted by Marin Manuel

Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.

• nidash
• 9 years ago - submitted by Greg Kiar

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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