Curator Dashboard

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 multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

• 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.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.

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• SciCrunch
• 9 years ago - submitted by Robert Butler

Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format.

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• SciCrunch
• 9 years ago - submitted by Scott Geib

Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.

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• RRID-Legacy
• 9 years ago - by Anonymous