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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://maltcms.sourceforge.net/users/features.html
An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics.
Proper citation: Maltcms (RRID:SCR_012057) Copy
http://insilicogenome.sourceforge.net/
A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations.
Proper citation: FIGG (RRID:SCR_012064) Copy
http://sourceforge.net/projects/diyg/
A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences.
Proper citation: DIYA (RRID:SCR_012066) Copy
http://fastphylo.sourceforge.net/
A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix.
Proper citation: Fastphylo (RRID:SCR_012068) Copy
http://mrbayes.sourceforge.net/
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
Proper citation: MrBayes (RRID:SCR_012067) Copy
http://sourceforge.net/projects/mmax2/
A GUI-based text annotation tool for creating and visualizing annotations.
Proper citation: MMAX2 (RRID:SCR_012100) Copy
http://ipapers.sourceforge.net/iPapers.html
Software application that manages many PDF files of articles, whose information can be obtained by PubMed.
Proper citation: iPapers (RRID:SCR_012103) Copy
http://sourceforge.net/projects/phylotreepruner/
A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.
Proper citation: PhyloTreePruner (RRID:SCR_012069) Copy
http://sourceforge.net/projects/coperead/
An efficient software tool to connect overlapping pair-end reads using k-mer frequencies.
Proper citation: Connecting Overlapped Pair-End reads (RRID:SCR_012102) Copy
http://sourceforge.net/projects/raspnmr/
Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy.
Proper citation: RASP (RRID:SCR_012062) Copy
http://sourceforge.net/projects/gsim/
Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
Proper citation: GSim (RRID:SCR_012061) Copy
http://sourceforge.net/projects/staden/
A C software implementation of SAM, BAM and CRAM file I/O.
Proper citation: Scramble (RRID:SCR_012036) Copy
http://mzmatch.sourceforge.net/mzmatch.R/mzmatch.ipeak.align.CowCoda.html
Software that performs retention time alignment on the given set of peaks.
Proper citation: CowCoDA (RRID:SCR_012039) Copy
http://sourceforge.net/projects/open-ms/
An algorithm to align LC-MS samples and to match corresponding ion species across samples.
Proper citation: OpenMS (RRID:SCR_012042) Copy
http://obi-warp.sourceforge.net/
Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.
Proper citation: OBI-Warp (RRID:SCR_012041) Copy
http://open-ms.sourceforge.net/
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.
Proper citation: TOPP (RRID:SCR_012044) Copy
http://open-ms.sourceforge.net/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm.
Proper citation: Antilope (RRID:SCR_012046) Copy
http://sourceforge.net/projects/swisspit/
Software for pipelined analysis of mass spectrometry data.
Proper citation: swissPIT (RRID:SCR_012045) Copy
http://sourceforge.net/projects/icplquant/
A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.
Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy
http://sourceforge.net/projects/mtoolbox/
Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.
Proper citation: MToolBox (RRID:SCR_012112) Copy
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