Showing 346 open source projects for "bio-bwa"

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  • 1
    ODD is a tool for optimal domain decomposition of atomic structure guided by the given molecular dynamics data.
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  • 2
    A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.
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  • 3
    pMap is an MPI-based tool to parallelize the alignment step of state-of-the-art sequence mapping programs. It allows transparent execution of the alignment step of a selected program in parallel on a compute-cluster.
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  • 4
    MetaBoFlux
    Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model.
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  • 5
    Flow Investigation using N-Dimensions
    Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.
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  • 6
    A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
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  • 7
    Similarity / dissimilarity measures for community ecologists, and palaeontologists.
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  • 8
    Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.
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  • 9
    Scanner based Bioparsers
    Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
    Downloads: 1 This Week
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  • 10
    BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.
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  • 11
    The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
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  • 12
    The project is for developing libraries for visualizing biological sequence data on the web. The libraries are written in C and currently use a language (lex/yacc) based front end for presenting features on genomes, contigs, or any type of sequence.
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  • 13
    MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
    Downloads: 0 This Week
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  • 14
    This software is developed by Kalidas (http://openwetware.org/wiki/Kalidas_Y) as part of his Ph.D. thesis. The method enables alignment of ligand molecules considered molecular graphs. It is useful in the domain of drug discovery and bioinformatics.
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  • 15
    A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.
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  • 16
    FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.
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  • 17
    Foad (EKG Processing)
    Foad is an open source software which receive an EKG Signal from scanner, WFDB database or heart sensors. Finding patient disease started by taking Fourier transform (FFT) from input signal and extract a single cycle. Based on some heuristic algorithm the most important feature like P , Q , R , S , T captured and feed to trained neural network. and so the final decision made by CNN library. As mentioned before this software also capable do some image processing on scanned paper to lower...
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  • 18
    PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y
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  • 19
    MTMP is a multi-threaded multiple pattern matching algorithm based on the Wu-Manber algorithm.
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  • 20
    The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
    Downloads: 0 This Week
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  • 21
    simple-galib
    This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.
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  • 22
    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.
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  • 23
    Simple static viewer of abnormal read pairs in second-generation alignment data.
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  • 24
    This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.
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  • 25
    MGFp
    MGFp is open parser implementation for the Mascot Generic Format (MGF). It uses bison/flex to define a formal grammar and provides the necessary C++ adapter classes. The software is provided under a BSD license. Development on SF.net has ceased. You can find the project at http://kirchnerlab.github.com/libmgf/
    Downloads: 0 This Week
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