Curator Dashboard

Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software suite of tools to build and search generalized profiles.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Java program for calculating patristic distances and graphically comparing the components of genetic change.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth