Bio-Informatics Software for Cygwin

Browse free open source Bio-Informatics software and projects for Cygwin below. Use the toggles on the left to filter open source Bio-Informatics software by OS, license, language, programming language, and project status.

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  • 1
    CONTIGuator
    CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
    Downloads: 2 This Week
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  • 2

    Nemo

    Individual-based forward-time genetics simulation software

    Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework.
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    Downloads: 2 This Week
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  • 3

    BayesAss

    Bayesian Inference of Recent Migration Using Multilocus Genotypes

    Inference of recent migration rates between populations using multi-locus marker genotype data.
    Downloads: 1 This Week
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  • 4
    JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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    Downloads: 1 This Week
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    Rent Manager Software

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  • 5
    APBS

    APBS

    Biomolecular electrostatics software

    This software has moved to http://www.poissonboltzmann.org/.
    Downloads: 0 This Week
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  • 6
    Allosteric Network Compiler
    A rule-based modelling framework for allosteric proteins and biochemical networks.
    Downloads: 0 This Week
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  • 7

    BIRAP

    Bacterial Intergenic Region Analysis Pipeline

    BIRAP (Bacterial Intergenic Region Analysis Pipeline) is an open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output from SAMtools for RNA-seq data and peptide/ePST locus file (GFF) from the Proteogenomic Mapping tool for prote-ogenomics data along with the genome and existing in silico annotation. When information regarding the locus of promot-ers and terminators in the genome (in .coords format) is pro-vided, the pipeline will also help identify non-coding RNA.
    Downloads: 0 This Week
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  • 8
    This is a collection of softwares that I have been using in my research on protein interaction network. By release them under the GPL 2.0 lience, I hope that they can be useful to others, as well.
    Downloads: 0 This Week
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  • 9

    CSST

    Cascade and Sharing Survival Trees, an ensemble for survival analysis

    Cascading and Sharing Survival Trees (CSST) is a tree-based enseble that allows to efficiently analize survival data. It is a strightforward extension of the CS4 method for lifetime collections of data. The CSST software comes along with its companion the CSST Prediction tool, to use the ensemble prediction in everyday life. Please, refer to the user's manual for further information.
    Downloads: 0 This Week
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  • 10

    Crux-Toolkit

    Software toolkit for tandem mass spectrometry analysis

    Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. If you use Crux in your research, please cite Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022--3027, 2008.
    Downloads: 0 This Week
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  • 11
    D-Tailor

    D-Tailor

    D-Tailor: automated analysis and design of DNA sequences

    Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of sequence analysis tools into a Monte-Carlo algorithm that evolves synthetic sequences towards user-defined goals.
    Downloads: 0 This Week
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  • 12

    DeNovoCheck

    DeNovoCheck: Inheritance analysis for NGS trio data

    DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants.
    Downloads: 0 This Week
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  • 13
    Bioinformatics software for analyzing the location of DNA motifs that induce self-catalytic depurination.
    Downloads: 0 This Week
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  • 14
    EMBOSS Suite
    EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
    Downloads: 0 This Week
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  • 15

    ENLY

    Bioinformatic tool to improve draft genome assemblies by closing gaps

    Downloads: 0 This Week
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  • 16
    HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
    Downloads: 0 This Week
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  • 17
    MCCCS

    MCCCS

    Multi Channel Classification and Clustering

    Here we present an image-based Multi Channel Classification and Clustering System (MCCCS). It is an generalized, script-based classification system for processing various kinds of image data. Due to the modular design, individual processing-components can be easily adapted, extended or exchanged by own extensions. See project website for installation instructions.
    Downloads: 0 This Week
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  • 18
    Matchup

    Matchup

    Bioinformatics tool for universal primers and group-specific probes

    Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment.
    Downloads: 0 This Week
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  • 19

    MutaNET

    NGS Pipeline and Automated Mutation Analysis

    MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance.
    Downloads: 0 This Week
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  • 20

    NHP-IMS

    Non-Human Primate Information Management System

    This project will enable a research lab using Non-Human Primates to control and track the Non-Human primates and the experiments associated with each.
    Downloads: 0 This Week
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  • 21
    Neurofitter is a parameter tuning package for electrophysiological neuron models. For more information please take a look at http://neurofitter.sourceforge.net
    Downloads: 0 This Week
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  • 22
    Patlac--Xml2cpp is a totally customizable code generator that generates classes (c++ for now) automatically from a xsd schema. Classes are described in google-ctemplate files and a xml options file allow precise definition of projects.
    Downloads: 0 This Week
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  • 23
    Piraña is a flexible modeling environment NONMEM and PsN.
    Downloads: 0 This Week
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  • 24
    PseAAC-Builder
    Description: PseAAC-Builder is a cross-platform stand-alone program for generating protein pseudo-amino acid compositions. This is a bioinformatics program. It performs faster than the existing PseAAC server. Reference: [1] Pufeng Du, Shuwang Gu, Yasen Jiao. PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets. International Journal of Molecular Sciences 15 (2014) pp.3495-3506 [2] Pufeng Du, Xin Wang, Chao Xu, Yang Gao. PseAAC-Builder: A cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. Analytical Biochemistry 425 (2012) pp.117-119
    Downloads: 0 This Week
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  • 25
    Downloads: 0 This Week
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